Debian Med Project
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Summary
Phylogeny
Debian Med phylogeny packages

This lists Debian packages related to phylogeny for use in life sciences. The purpose of this compilation of packages is to have a handy subset of from the med-bio metapackage which contains a lot more than only phylogeny related software.

Description

For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:

If you discover a project which looks like a good candidate for Debian Med to you, or if you have prepared an unofficial Debian package, please do not hesitate to send a description of that project to the Debian Med mailing list

Links to other tasks

Debian Med Phylogeny packages

Official Debian packages with high relevance

Altree
Program til at udføre fylogeni-baserede forenings- og lokaliseringsanalyse
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ALTree var designet til at udføre associationsdetektering og lokalisering af modtagelighedssider ved hjælp af haplotype-fylogenetiske træer: for det første så giver det mulighed for detektering af en association mellem et kandidatgen og en sygdom, og for det andet gør det muligt at lave en hypotese om modtagelighedsloci.

Please cite: Claire Bardel, Vincent Danjean and Emmanuelle Genin: ALTree: association detection and localization of susceptibility sites using haplotype phylogenetic trees. (PubMed,eprint) Bioinformatics 22(11):1402-1403 (2006)
Registry entries: SciCrunch  OMICtools 
Beast-mcmc
Bayesiansk MCMC-fylogenetisk inferens
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BEAST er et program til bayesiansk MCMC-analyse af molekylære sekvenser udviklet til flere platforme. Det er orienteret mod rodfæstede, tidsmålte fylogenier udledt ved hjælp af strenge eller afslappede molekylære urmodeller. Det kan anvendes som en fremgangsmåde til at rekonstruere fylogenier men er også en ramme til afprøvning af evolutionære hypoteser uden konditionering på en enkelt trætopologi. BEAST bruger MCMC til at lave et gennemsnit over træplads, således at hvert træ er vægtet proportional med dens senere sandsynlighed. Inkluderet er en simpel brugerflade til opsætning af standardanalyser og en række programmer til at analysere resultaterne.

The package is enhanced by the following packages: beast-mcmc-doc beast-mcmc-examples
Please cite: Alexei J Drummond and Andrew Rambaut: BEAST: Bayesian evolutionary analysis by sampling trees. (PubMed,eprint) BMC Evol Biol 8(7):214 (2007)
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Clustalw
Global nukleotid eller peptid sekvensjustering
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Dette program udfører en sammenligning af flere nukleotid- eller aminosyresekvenser. Det genkender formatet for inddatasekvenser, og om sekvenser er nukleinsyre (DNA / RNA) eller aminosyre (proteiner). Uddataformatet kan vælges i forskellige formater for flere sammenligninger såsom Phylip eller FASTA. Clustal W er velaccepteret.

Produktionen af ​​Clustal W kan redigeres manuelt, men helst med et justeringssredigeringsprogram som SeaView eller indenfor dens følgesvend Clustal X. Når man bygger en model fra din sammenligning, kan denne anvendes til forbedrede databasesøgninger. Debianpakken HMMER skaber en sådan i form af en HMM.

The package is enhanced by the following packages: clustalw-mpi
Please cite: M. A. Larkin, G. Blackshields, N. P. Brown, R. Chenna, P. A. McGettigan, H. McWilliam, F. Valentin, I.M. Wallace, A. Wilm, R. Lopez, J. D. Thompson, T. J. Gibson and D. G. Higgins: Clustal W and Clustal X version 2.0. (PubMed,eprint) Bioinformatics 23(21):2947-2948 (2007)
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Clustalx
Flere sammenligninger af nukledie syre- og proteinsekvenser - grafisk brugerflade
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Denne pakke tilbyder en grafisk brugerflade for Clustals program for sekvenssammenligning. Det tilbyder et integreret miljø for udførsel af flere sekvens- og profilsammenligninger for at analysere resultaterne.

Menuen i rullegardinet øverst i vinduet giver dig mulighed for at vælge alle indstillinger krævet for traditionel flersekvens- og profilsammenligning. Du kan klippe og indsætte sekvenser for at ændre rækkefølgen for sammenligningen; du kan vælge et undersæt af sekvenser der skal sammenlignes; du kan vælge et underinterval af sammenligningen der kan rettes ud og indsættes tilbage i den originale sammenligning.

En sammenlignende kvalitetsanalyse kan udføres og lavt bedømte segmenter eller exceptionelle rester kan fremhæves.

Please cite: M.A. Larkin, G. Blackshields, N.P. Brown, R. Chenna, P.A. McGettigan, H. McWilliam, F. Valentin, I.M. Wallace, A. Wilm, R. Lopez, J.D. Thompson, T.J. Gibson and D.G. Higgins: Clustal W and Clustal X version 2.0. (PubMed,eprint) Bioinformatics 23(21):2947-2948 (2007)
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Dialign
Segmentbaseret flersekvensjustering
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DIALIGN2 er et kommandolinjeværktøj som kan gennemføre justering af flere protein- eller DNA-sekvenser. Det konstruerer justeringer med gabsfrie par af modsvarende segmenter fra sekvenserne. Dette rangeringsskema for justeringer er den grundlæggende forskel mellem DIALIGN og andre globale eller lokale justeringsmetoder. Bemærk at DIALIGN ikke gør brug af nogen sanktioner over for gab.

Please cite: Burkhard Morgenstern: DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. (PubMed,eprint) Bioinformatics 15(3):211-218 (1999)
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Dialign-tx
Segmentbaseret flersekvensjustering
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DIALIGN-TX er et kommandolinjeværktøj til udførsel af flerjustering af protein- eller DNA-sekvenser. Det er en fuldstændig reimplementering af den segmentbaserede fremgangsmåde inklusiv flere nye forbedringer og heuristik som forbedrer kvaliteten af uddatajusteringer væsentligt sammenlignet med DIALIGN 2.2 og DIALIGN-T. For parvis justering bruger DIALIGN-TX en algoritme til fragmentkædning som favoriserer kæder med lave resultater for lokale justeringer over isolerede fragmenter med høje resultater. For flerjustering bruger DIALIGN-TX en forbedret grådig procedure som er mindre følsom for falske lokale sekvensensheder.

The package is enhanced by the following packages: dialign-tx-data
Please cite: Amarendran R. Subramanian, Michael Kaufmann and Burkhard Morgenstern: DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment. (PubMed) Algorithms for Molecular Biology 3(1):6 (2008)
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Exonerate
generisk værktøj til parvis sekvenssammenligning
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Exonerate tillader justering af sekvenser via en model med flere justeringer, der bruger enten udførlig dynamisk programmering eller en variation af heuristiker. De meste af funktionaliteten i den dynamsike Wiseprogrammeringspakke blev erstattet med C for bedre effektivitet. Exonerate er en tilhørende komponent i opbygningen af databaserne Ensembl genome, der tilbyder sammenligningsoversigter mellem RNA- og DNA-sekvenser og dermed afgør opdelingsvariationer og kodesekvenser generelt.

Et simulationssystem In-silico PCR Experiment (se manualsiden for ipcress) pakkes med exonerate.

Denne pakke kommer også med et udvalg af redskaber til udførelse af enkle og hurtige manipulationer på fasta-filer over 2 Gb.

Please cite: Guy C. Slater and Ewan Birney: Automated generation of heuristics for biological sequence comparison. (PubMed,eprint) BMC Bioinformatics 6(1):31 (2005)
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Fastdnaml
Værktøj for konstruktion af fylogentiske træer for DNA-sekvenser
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fastDNAml er et program afledt fra Joseph Felsensteins version 3.3 DNAML (del af hans PHYLIP-pakke). Bruger bør konsultere dokumentationen for DNAML før de bruger dette program.

fastDNAml er et forsøg på at løse det samme problem som DNAML, men at gøre dette hurtigere og med mindre brug af hukommelse, så at større træer og/eller flere bootstrap-replikater kan håndteres. Meget af fastDNAml er bare en genindspilning af PHYLIP 3.3 DNAML-programmet fra PASCAL til C.

Bemærk at dette programs hjemmeside ikke længere er tilgængeligt og at dette program derfor nok ikke vil se yderligere opdateringer.

Please cite: Gary J. Olsen, Hideo Matsuda, Ray Hagstrom and Ross Overbeek: fastDNAml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. (PubMed,eprint) Comput Appl Biosci 10(1):41-48 (1994)
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Figtree
Grafisk fylogenetisk træfremviser
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FigTree er designet som en grafisk fremviser af fylogenetiske træer og som et program til at fremstille udgivelsesklare figurer. Det er specielt designet til at vise summerede og kommenterede træer fremstillet af BEAST.

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Hmmer
Profilskjulte Markov-modeller for proteinsekvensanalyse
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HMMER er en implementering af profilskjulte Markov-modelmetoder for sensitive søgninger i biologiske sekvensdatabaser med brug af flersekvensjusteringer som forespørgsler.

Givet en flersekvensjustering som input, bygger HMMER en statistisk model kaldt »skjult Markovmodel«, som kan bruges som en forespørgsel ind i en sekvensdatabase for at finde (og/eller justere) yderligere homologier for sekvensfamilien.

Please cite: S. R. Eddy: Profile hidden Markov models. (PubMed,eprint) Bioinformatics 14(9):755-763 (1998)
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Iqtree
Effektivt fylogenetisk program ved maksimal sandsynlighed
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IQ-TREE er et meget effektivt maksimal sandsynlighedsfylogenetisk program med følgende nøglefunktioner blandt flere:

  • En hidtil ukendt hurtig og effektiv stokastisk algoritme til at estimere maksimale sandsynlighedstræer. IQ-TREE overgår både RAxML og PhyML i form af sandsynlighed, men kræver tilsvarende mængde beregning (se Nguyen et al., 2015)
  • En ultrahurtig bootstrap-tilnærmelse til at vurdere branchestøtter (se Minh et al., 2013)
  • En bred vifte af substitutionsmodeller for binær, DNA, protein, codon, og morfologiske tilpasninger
  • Ultrahurtig model valg for alle datatyper, 10 til 100 gange hurtigere end jModelTest og ProtTest
  • Find bedste partitionsskema ligesom PartitionFinder
  • Partitioneret modeller med blandede datatyper for fylogenetiske (multigenfamilier) sammenligninger, der giver mulighed for separate, proportionale, eller fælles grenlængder blandt gener
  • Støtte til fylogenetisk sandsynlighedsbibliotek (PLL) (se Flouri et al., 2014)
Please cite: Lam Tung Nguyen, Heiko A. Schmidt, Arndt von Haeseler and Bui Quang Minh: IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. (PubMed,eprint) Mol. Biol. Evol. 32(1):268-274 (2015)
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Jmodeltest
HPC-udvalg af modeller for nukleotid substitution
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jModelTest er et værktøj til at udføre statistisk valg af bedst egnede modeller for nukleotidsubstitution. Værktøjet gennemfører fem forskellige modelselektionsstrategier: hierarkiske og dynamiske sandsynlighedskvotienttest (hLRT og dLRT), Akaike og bayesianske oplysningskriterier (AIC og BIC), og en beslutningsteorimetode (DT). Det giver også skøn over modeludvælgelsesusikkerheden, parametervigtighed og model-gennemsnit parameterestimater, herunder model-gennemsnit for trætopologier. jModelTest 2 omfatter High Performance Computing-funktioner (HPC) og ekstra funktioner som nye strategier for træoptimering, model- gennemsnit fylogenetiske træer (både topologi- og grenlængde), heuristisk filtrering og automatisk logning af brugeraktivitet.

Please cite: Diego Darriba, Guillermo L Taboada, Ramón Doallo and David Posada: jModelTest 2: more models, new heuristics and parallel computing. (PubMed) Nature Methods 9(8):772 (2012)
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Kalign
Global og progressiv flersekvensjustering
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Kalign er et kommandolinjeværktøj til at udføre flerjustering af biologiske sekvenser. Den bruger Muth-Manbers algoritme til strengmatchning, både til at forbedre præcisionen og hastigheden for justeringen. Den bruger global, progressiv justeringsfremgangsmåde, forbedret ved at bruge en omtrentlig strengmatchende algoritme til at beregne sekvensafstande og ved at indarbejde lokale matchninger i den ellers globale justering.

Please cite: Timo Lassmann, Oliver Frings and Erik L. L. Sonnhammer: Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features. (PubMed,eprint) Nucl. Acids Res. 37(3):858-865 (2009)
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Mrbayes
Bayesiansk inferens for fylogeni
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Bayesiansk inferens for fylogeni er baseret på en kvantitet kaldt den posterior sandsynlighedsfordeling for træer, som er sandsynligheden for et træ betinget af observationerne. Den betingelse opnås ved hjælp af Bayes sætning. Den posterior sandsynlighedsfordeling for træer er umuligt at beregne analytisk; i stedet, bruger MrBayes en simuleringsteknik kaldet Markov chain Monte Carlo (eller MCMC) at tilnærme posteriore sandsynligheder af træer.

The package is enhanced by the following packages: mrbayes-doc
Please cite: Fredrik Ronquist, Maxim Teslenko, Paul van der Mark, Daniel L. Ayres, Aaron Darling, Sebastian Höhna, Bret Larget, Liang Liu, Marc A. Suchard and John P. Huelsenbeck: MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice across a Large Model Space. (PubMed,eprint) Systematic Biology (2012)
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Muscle
Flerjusteringsprogram for proteinsekvenser
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MUSCLE er et flerjusteringsprogram for proteinsekvenseer. MUSCLE står for flersekvenssammenligning efter log-forventning. I forfatternes test opnåede MUSCLE den højeste pointgivning af alle testede programmer i flere målinger for forskellige justeringspræcisioner, og programmet er også et af de hurtigste programmer på markedet.

Please cite: Robert C. Edgar: MUSCLE: multiple sequence alignment with high accuracy and high throughput. (PubMed,eprint) Nucleic Acids Research 32(5):1792-1797 (2004)
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Topics: Sequence analysis
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Mustang
strukturel justering på flere måder af proteiner
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Mustang er en algoritme til justering af flere proteinstrukturer. Givet et sæt af PDB-filer, bruger programmet den rumlige information i Calpha-atomer hos sættet til at producere en sekvensjustering. Baseret på en progressiv parvis heuristik fortsætter algoritmen så igennem et antal raffineringsgennemløb. Mustang rapporterer den flertydige sekvensjustering og den tilsvarende superplacering af strukturer.

The package is enhanced by the following packages: mustang-testdata
Please cite: Arun S. Konagurthu, James C. Whisstock, Peter J. Stuckey and Arthur M. Lesk: MUSTANG: A multiple structural alignment algorithm. (PubMed) Proteins: Structure, Function, and Bioinformatics 64(3):559-574 (2006)
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Njplot
Fylogenetisk trætegningsprogram
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NJplot kan tegne ethvert dendrogram, der kan udtrykkes i det almindelige polygene træformat (f.eks. det format, der bruges af Phylip-pakken). NJplot

 er især praktisk for fæstnede og ikke-fæstnede træer fra
træopbygningsmetoderne parsimony, afstand eller maximum-likelihood.
Please cite: G. Perrière and M. Gouy: WWW-query: An on-line retrieval system for biological sequence banks. (PubMed) Biochimie 78(5):364–369 (1996)
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Phylip
Programpakke for udledning af fylogenier
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PHYLogeny Inference Package er en programpakke for udledning af fylogenier (evolutionstræer) fra sekvenser. Tilgængelige metoder i pakken inkluderer parsimony, afstandsmatrix og sandsynlighedsmetoder, inklusive bootstrapping og konsensustræer. Datatyper som kan håndteres inkluderer molekylære sekvenser, genfrekvenser, begrænsningssider, afstandsmatricer og 0/1 diskrete tegn.

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Phyml
Fylogenisk estimering der bruger maksimum lIkelihood
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PhyML er et program, som estimerer maksimum likelihood-fylogenier baseret på sammenligninger af nukleotid- eller aminosyresekvenser. Programmet tilbyder en bred vifte af indstillinger, som blev designet til at lette fylogentiske standardanalyser. PhyML's største styrke ligger i det store antal erstatningsmodeller koblet til diverse indstillinger for søgning i rummet med fylogenetiske trætopologier, der går fra meget hurtige og effektive metoder til langsommere, men mere præcise fremgangsmåder. Programmet implementerer også to metoder til at evaluere grenunderstøttelser i en god statistisk ramme (den ikkeparametriske bootstrap og den tilnærmede likelihood-forholdstest).

PhyMl blev designet til at behandle moderate til store datasæt. I teorien kan sammenligninger med op til 4.000 sekvenser og længde op til 2.000.000 tegn analyseres. I praksis er mængden af hukommelse til at behandle et datasæt proportional med produktet af antallet af sekvenser og deres længde. Et stort antal sekvenser kan derfor kun behandles, såfremt de er korte. PhyMl kan også håndtere lange sekvenser, så længe der ikke er mange. Med de fleste standardcomputere er komfortzonen for PhyML generelt omkring 3 til 500 sekvenser, som er mindre end 2.000 tegn lange.

Denne pakke inkluderer også PhyTime.

Please cite: Stéphane Guindon: Bayesian estimation of divergence times from large sequence alignments. (PubMed,eprint) Molecular Biology and Evolution 27(8):1768-81 (2010)
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Poa
Partial Order Alignment for flere sekvenssammenligninger
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POA er Partial Order Alignment, et hurtigt program for flere sekvenssammenligninger (MSA) i bioinformatik. Dets fordele er hastighed, skalabilitet, sensitivitet og den overlegne evne til at håndtere forgrening/indels i sammenligningen. Delvis rækkesammenligning er en tilgang til MSA, som kan kombineres med de eksisterende metoder, såsom gradvis sammenligning. POA sammenligner optimalt et par MSA'er, og kan derfor anvendes direkte til progressive sammenligningsmetoder såsom CLUSTAL. For store sammenligninger er Progressive POA 10-30 gange hurtigere end CLUSTALW.

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Populations
Program til befolkningsgenetik
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Populations er et program til befolkningsgenetik. Det beregner genetiske afstande mellem befolkninger eller individuelle personer. Det bygger fylogenetiske træer (NJ eller UPGMA) med boostrap-værdier.

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Proalign
Probabilistic multiple alignment program
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ProAlign performs probabilistic sequence alignments using hidden Markov models (HMM). It includes a graphical interface (GUI) allowing to (i) perform alignments of nucleotide or amino-acid sequences, (ii) view the quality of solutions, (iii) filter the unreliable alignment regions and (iv) export alignments to other software.

ProAlign uses a progressive method, such that multiple alignment is created stepwise by performing pairwise alignments in the nodes of a guide tree. Sequences are described with vectors of character probabilities, and each pairwise alignment reconstructs the ancestral (parent) sequence by computing the probabilities of different characters according to an evolutionary model.

Please cite: Ari Löytynoja and Michel C Milinkovitch: A hidden Markov model for progressive multiple alignment. (PubMed,eprint) Bioinformatics 19(12):1505-13 (2003)
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Probalign
Multiple sekvensjustering med brug partitionsfunktionel posteriore sandsynligheder
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Probalign bruger estimater, fra partitionsfunktionelle posteriore sandsynligheder, til at beregne den maksimale præcision for multiple sekvensjusteringer. Den yder statistisk set betydeligt bedre end de ledende justeringsprogrammer Probcons v1.1, MAFFT v5.851 og MUSCLE v3.6 i ydelsesmålinger fra BAliBASE 3.0, HOMSTRAD og OXBENCH. Forbedringerne med Probalign er størst på datasæt, der indeholder udvidelser til N/C- terminalen, og på datasæt med sekvenser som er lange sekvenser og har heterogene længder. Med datasæt bestående af heterogene længder, der indeholder gentagelser, er præcisionen for Probalign 10 % og 15 % højere end de andre tre metoder, når standardafvigelse på længden er mindst 300 og 400.

Please cite: Usman Roshan and Dennis R. Livesay: Probalign: multiple sequence alignment using partition function posterior probabilities. (PubMed,eprint) Bioinformatics 22(22):2715-21 (2006)
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Probcons
flersekvens-sammenstilling baseret på probabilistisk konsistens (PROBabilistic CONSistency)
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Værktøj til at fremstille flere sammenstillinger af proteinsekvenser. Med brug af probabilistiske modelleringer og teknikker til konsistensbaserede sammenstillinger, har PROBCONS opnået den højeste nøjagtighed blandt alle sammenstillingsmetoder til dato. I BAliBASE-databasen med sammenligninger af sammenstillinger, viser sammenstillinger fremstillet af PROBCONS statistisk signifikante forbedringer i forhold til andre aktuelle programmer, indeholdende i gennemsnit 7% flere korrekt sammenstillede kolonner end de som stammer fra T-Coffee, 11% flere korrekt sammenstillede kolonner end dem fra CLUSTAL W, og 14% mere korrekt sammenstillede kolonner end dem fra DIALIGN.

Please cite: Chuong B. Do, Mahathi S.P. Mahabhashyam, Michael Brudno and Serafim Batzoglou: ProbCons: Probabilistic consistency-based multiple sequence alignment. (PubMed,eprint) Genome Research 15(2):330-340 (2005)
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Proda
multi-sammenligning af protein-sekvenser
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ProDA er et system til automatiseret detektering og sammenligning af homologe regioner i kollektioner af proteiner med arbitrære domæne- arkitekturer. Givent et input sæt af ikke-sammenlignede sekvenser, vil ProDA identificere alle homologe regioner som fremkommer i en eller flere sekvenser, og returnerer en kollektion af lokale flerjusteringer for disse regioner.

Please cite: Tu Minh Phuong, Chuong B. Do, Robert C. Edgar and Serafim Batzoglou: Multiple alignment of protein sequences with repeats and rearrangements. (PubMed,eprint) Nucl. Acids Res. 34(20):5932-5942 (2006)
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Prottest
selection of best-fit models of protein evolution
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PROTTEST (ModelTest's relative) is a program for selecting the model of protein evolution that best fits a given set of sequences (alignment). This java program is based on the Phyml program (for maximum likelihood calculations and optimization of parameters) and uses the PAL library as well. Models included are empirical substitution matrices (such as WAG, LG, mtREV, Dayhoff, DCMut, JTT, VT, Blosum62, CpREV, RtREV, MtMam, MtArt, HIVb, and HIVw) that indicate relative rates of amino acid replacement, and specific improvements (+I:invariable sites, +G: rate heterogeneity among sites, +F: observed amino acid frequencies) to account for the evolutionary constraints impossed by conservation of protein structure and function. ProtTest uses the Akaike Information Criterion (AIC) and other statistics (AICc and BIC) to find which of the candidate models best fits the data at hand.

Please cite: Diego Darriba, Guillermo L. Taboada, Ramón Doallo and David Posada: ProtTest 3: fast selection of best-fit models of protein evolution. (PubMed,eprint) Bioinformatics 27(8):1164-5 (2011)
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Seaview
Grænseflade til flere platforme for sekvenssammenligning og fylogeni
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SeaView læser og skriver diverse filformater (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE, Newick) for DNA og proteinsekvenser og af fylogenetiske træer. Sammenligninger kan redigeres manuelt. SeaView driver programmerne Muscle eller Clustal Omega for flere sekvenssammenligninger, og giver også mulighed for at bruge alle eksterne sammenligningsalgoritmer, som kan læse og skrive FASTA-formaterede filer. Programmet beregner fylogenetiske træer og sparer på ressourcerne ved at bruge PHYLIP's dnapars/protpars-algoritmen, på afstand med NJ- eller BioNJ-algoritmer på en række evolutionære afstande, eller ved maximum likelihood via programmet PhyML 3.0. SeaView tegner fylogenetiske træer på skærmen eller til PostScript-filer, og giver mulighed for at hente sekvenser fra EMBL/GenBank/UniProt via internettet.

The package is enhanced by the following packages: muscle
Please cite: Manolo Gouy, Stephane Guindon and Olivier Gascuel: SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. (PubMed,eprint) Mol Biol Evol 27(2):221-224 (2010)
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Sigma-align
Simpel grådig flerjustering af ikke-kodende DNA-sekvenser
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Sigma (»Simple greedy multiple alignment«, simpel grådig flerjustering) er et justeringsprogram. Dets algoritme og scoringsskema er designet specifikt til ikke-kodende DNA-sekvenser.

Den bruger en strategi til søgning efter bedst mulige, gabsfrie, lokale justeringer. Dette sker ved hvert trin, for at gøre den bedst mulige justering konsistent med eksisterende justeringer. Den scorer signifikansen af justeringen baseret på længden af de justerede fragmenter og en baggrundsmodel. Disse kan tildeles eller estimeres fra en tillægsfil med intergenisk DNA.

Please cite: Siddharthan, Rahul: Sigma: multiple alignment of weakly-conserved non-coding DNA sequence. (PubMed) BMC Bioinformatics 7(1):143 (2006)
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Spread-phy
Analyser og visualiser fylogeografiske rekonstruktioner
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SPREAD er et brugervenligt program til at analysere og visualisere fylogeografiske rekonstruktioner, der er et resultat af bayesiansk indledning af spatio-temporal diffusion.

Der er en øvelse for SPREAD på nettet http://www.kuleuven.be/aidslab/phylogeography/tutorial/spread_tutorial.html

Oprindelig er dette program navngivet »spread«. Der er dog allerede en sådan pakke i Debian og derfor blev et »phy« for phylogeny tilføjet.

Please cite: Filip Bielejec, Andrew Rambaut, Marc A. Suchard and Philippe Lemey: SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics. (PubMed,eprint) Bioinformatics 27(20):2910-2912 (2011)
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T-coffee
Flersekvensjustering
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T-Coffee er en pakke for flersekvensjustering. Givet et sæt af sekvenser (proteiner eller DNA) opretter T-Coffee en flersekvensjustering. Version 2.00 og højere kan mikse sekvenser og strukturer.

T-Coffee tillader kombinationen af flere/parvise, globale eller lokale justeringer i en enkel model. Programmet kan også estimere konsistensniveauet for hver placering i den nye justering med resten af justeringen. Se pre-print for yderligere information.

T-Coffee har en variant kaldet M-Coffee som gør det muligt at kombinere uddata af mange flersekvensjusteringspakker. I sin udgivet version bruger den MUSCLE, PROBCONS, POA, DiAlign-TS, MAFFT, Clustal W, PCMA og T-Coffee. En speciel version er blevet lavet for Debian, DM-Coffee, som kun bruger frie programmer ved at erstatte Clustal W med Kalign. Brug af 8 Methods for M-Coffee kan undertiden være ret tungt. Du kan bruge et undersæt af dine favoritmetoder, hvis du foretrækker dette.

The package is enhanced by the following packages: clustalw dialign-tx kalign mafft muscle ncbi-blast+ poa prank probcons tm-align
Please cite: Cédric Notredame, Desmond G. Higgins and Jaap Heringa: T-coffee: a novel method for fast and accurate multiple sequence alignment. (PubMed) Journal of Molecular Biology 302(1):205-217 (2000)
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Tm-align
Strukturel sammenligning af proteiner
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TM-align er en computeralgoritme for sammenligning af proteinstruktur, der bruger dynamisk programmering. Bedømmelsen udføres af TM-scores rotationsmatrix. Dette svarer til RMSD i forhold til ujusterede dele af strukturen der influerer bedømmelsen mindre end de mere strukturelle bevarede regioner.

Please cite: Yang Zhang and Jeffrey Skolnick: TM-align: A protein structure alignment algorithm based on TM-score. (PubMed,eprint) Nucleic Acids Research 33(7):2302-2309 (2005)
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Tree-ppuzzle
Paralleliseret rekonstruktion af fylogenetiske træer gennem maksimal lighed
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TREE-PUZZLE (det nye navn for PUZZLE) er et interaktivt konsolprogram, der implementerer en hurtig algoritme for træ-søgning, kvartets-gåder (»quartet-puzzling«), der tillader analyse af større datasæt og automatisk tildeling af estimater af understøttelse for hver enkelt interne gren. TREE-PUZZLE beregner også parvist sandsynligheden for maksimale distancer, og desuden længden på grene for træer angivet af bruger. Længde på grene kan også beregnes med antagelsen af et ur (»clock-assumption«). Yderligere tilbyder TREE-PUZZLE en ny metode, ligheds-kortlægning, til at undersøge understøttelsen af hypotese-baserede interne grene uden beregning af træet i sin helhed, samt visualisering af det fylogenetistiske indhold af sekvensjusteringer.

Dette er den paralleliserede version af tree-puzzle.

Please cite: Heiko A. Schmidt, Korbinian Strimmer, Martin Vingron and Arndt von Haeseler: TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. (PubMed,eprint) Bioinformatics 18(3):502-504 (2002)
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Tree-puzzle
Rekonstruktion af fylogenetiske træer gennem maksimal lighed
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TREE-PUZZLE (det nye navn for PUZZLE) er et interaktivt konsolprogram, der implementerer en hurtig algoritme for træ-søgning, kvartets-gåder (»quartet-puzzling«), der tillader analyse af større datasæt og automatisk tildeling af estimater af understøttelse for hver enkelt interne gren. TREE-PUZZLE beregner også parvist sandsynligheden for maksimale distancer, og desuden længden på grene for træer angivet af bruger. Længde på grene kan også beregnes med antagelsen af et ur (»clock-assumption«). Yderligere tilbyder TREE-PUZZLE en ny metode, ligheds-kortlægning, til at undersøge understøttelsen af hypotese-baserede interne grene uden beregning af træet i sin helhed, samt visualisering af det fylogenetistiske indhold af sekvensjusteringer.

Please cite: Heiko A. Schmidt, Korbinian Strimmer, Martin Vingron and Arndt von Haeseler: TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. (PubMed,eprint) Bioinformatics 18(3):502-504 (2002)
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Treeview
Ny Javaimplementering af Michael Eisens TreeView
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TreeView opretter en matrixlignende visning af udtryksdata, kendt som Eisenklyngedannelse. Den originale implementering var et Windowsprogram navngivet TreeView af Michael Eisen. Denne TreeView-pakke, undertiden refereret som jTreeView, blev skrevet om i Java under en fri licens.

Java TreeView er en fremviser for microarray-data i PCL- eller CDT-format, som kan udvides.

Please cite: Alok J. Saldanha: Java Treeview -- extensible visualization of microarray data. (PubMed,eprint) Bioinformatics 20(17):3246-3248 (2004)
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Treeviewx
Viser og udskriver fylogenetiske træer
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TreeView X er et open source program for flere platforme til at vise fylogenetiske træer. Programmet kan læse og vise træfiler i NEXUS- og Newickformatet (såsom uddata fra PAUP*, ClustalX, TREE-PUZZLE og andre programmer). Programmet tillader en at sortere trægrene og at eksportere træerne i SVG-format.

Please cite: Page, Roderic D. M.: TreeView: an application to display phylogenetic trees on personal computers. (PubMed) Comput. Appl. Biosci. 12(4):357-8 (1996)
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Official Debian packages with lower relevance

Python3-treetime
inference of time stamped phylogenies and ancestral reconstruction (Python 3)
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TreeTime provides routines for ancestral sequence reconstruction and the maximum likelihoo inference of molecular-clock phylogenies, i.e., a tree where all branches are scaled such that the locations of terminal nodes correspond to their sampling times and internal nodes are placed at the most likely time of divergence.

TreeTime aims at striking a compromise between sophisticated probabilistic models of evolution and fast heuristics. It implements GTR models of ancestral inference and branch length optimization, but takes the tree topology as given. To optimize the likelihood of time-scaled phylogenies, treetime uses an iterative approach that first infers ancestral sequences given the branch length of the tree, then optimizes the positions of unconstraine d nodes on the time axis, and then repeats this cycle. The only topology optimization are (optional) resolution of polytomies in a way that is most (approximately) consistent with the sampling time constraints on the tree. The package is designed to be used as a stand-alone tool or as a library used in larger phylogenetic analysis workflows.

Features

  • ancestral sequence reconstruction (marginal and joint maximum likelihood)
  • molecular clock tree inference (marginal and joint maximum likelihood)
  • inference of GTR models
  • rerooting to obtain best root-to-tip regression
  • auto-correlated relaxed molecular clock (with normal prior)

This package provides the Python 3 module.

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Debian packages in contrib or non-free

Gmap
spliced and SNP-tolerant alignment for mRNA and short reads
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This package contains the programs GMAP and GSNAP as well as utilities to manage genome databases in GMAP/GSNAP format. GMAP (Genomic Mapping and Alignment Program) is a tool for aligning EST, mRNA and cDNA sequences. GSNAP (Genomic Short-read Nucleotide Alignment Program) is a tool for aligning single-end and paired-end transcriptome reads. Both tools can use a database of

  • known splice sites and identify novel splice sites.
  • known single-nucleotide polymorphisms (SNPs). GSNAP can align bisulfite-treated DNA.
Please cite: Thomas D. Wu and Colin K. Watanabe: GMAP: a genomic mapping and alignment program for mRNA and EST sequences. (eprint) Bioinformatics 21(9):1859-1875 (2005)
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Packaging has started and developers might try the packaging code in VCS

Forester
Graphical vizualiation tool Archaeopteryx
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Archaeopteryx is a software tool for the visualization, analysis, and editing of potentially large and highly annotated phylogenetic trees. It can be used both as applet (ArchaeopteryxA and ArchaeopteryxE) and as a standalone application.

Patristic
Calculate patristic distances and comparing the components of genetic change
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Patristic overcomes some logistic barriers to analysing signals in sequences. In additional to calculating patristic distances, it provides plots for any combination of matrices, calculates commonly used statistics, allows data such as isolation dates to be entered and reorders matrices with matching species or gene labels. It will be used to analyse rates of mutation and substitutional saturation and the evolution of viruses.

Please cite: Mathieu Fourment and Mark J Gibbs: PATRISTIC: a program for calculating patristic distances and graphically comparing the components of genetic change. (PubMed,eprint) BMC Evolutionary Biology 6:1 (2006)

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Phylowin - wnpp
Graphical interface for molecular phylogenetic inference
License: unknown
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Phylo_win is a graphical colour interface for molecular phylogenetic inference. It performs neighbor-joining, parsimony and maximum likelihood methods and bootstrap with any of them. Many distances can be used including Jukes & Cantor, Kimura, Tajima & Nei, HKY, Galtier & Gouy (1995), LogDet for nucleotidic sequences, Poisson correction for protein sequences, Ka and Ks for codon sequences. Species and sites to include in the analysis are selected by mouse. Reconstructed trees can be drawn, edited, printed, stored and evaluated according to numerous criteria.

This program uses sources files from the Phylip program, which forbids its use for profit. Therfore, Phylo_win will unfortunately have to be distributed in contrib or non-free.

Remark of Debian Med team: Issuer of previous ITP said:

Because I could never figure out the license of Phylo_win, and because the upstream authors released SeaView 4, which provides similar functionalities, I will not package Phylo_win.

Probably it makes sense to remove this project from the prospective packages list.

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Gbioseq
DNA sequence editor for Linux
License: GPL
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gBioSeq is in an early stage of development, but it is already running. The goal is to provide an easy to use software to edit DNA sequences under Linux, Windows, MacOsX, using GTK C# (Mono).

Jstreeview
Editor for Phylogenetic Trees
License: MIT/X11
Debian package not available
Language: JavaScript

A concise viewer/editor for phylogenetic trees in the Newick format. The core functions are written in JavaScript, using the canvas tag proposed by HTML 5. No server side support is needed for rendering the picture and therefore you can grab this page together with knhx.js and canvastext.js to locally view your trees in a supported web browser.

The source can be downloaded at http://www.sanger.ac.uk/Users/lh3/download/jstreeview.zip

Phpphylotree
draw phylogenetic trees
License: GPL
Debian package not available

PhpPhylotree is a web application that is able to draw phylogenetic trees. It produces an SVG (Scalable Vector Graphic) file from phylip/newick tree files.

Treetime
Bayesian sampling of phylogenetic trees from molecular data
License: GPL
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TreeTime is controlled by input files in nexus format and does bayesian sampling of phylogenetic trees from these data.

*Popularitycontest results: number of people who use this package regularly (number of people who upgraded this package recently) out of 200178