Starting With Phylemon

ClustalW

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
Thompson JD, Higgins DG, Gibson TJ
Nucleic Acids Res22p4673-80(1994 Nov 11)

Muscle

MUSCLE: multiple sequence alignment with high accuracy and high throughput.
Edgar RC
Nucleic Acids Res32p1792-7(2004)

Lagan and M-Lagan

LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA.
Brudno M, Do CB, Cooper GM, Kim MF, Davydov E, Green ED, Sidow A, Batzoglou S
Genome Res13p721-31(2003 Apr)

MrBayes

MrBayes 3: Bayesian phylogenetic inference under mixed models.
Ronquist F, Huelsenbeck JP
Bioinformatics19p1572-4(2003 Aug 12)

PHYLIP (including TreeDist)

PHYLIP (Phylogeny Inference Package) version 3.6.
Felsenstein, J.
Distributed by the author. Department of Genome Sciences, University of Washington, Seattle (USA) (2004)

TREE-Puzzle

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing.
Schmidt HA, Strimmer K, Vingron M, von Haeseler A
Bioinformatics18p502-4(2002 Mar)

NJ trees using ML distances (HYPHY)

HyPhy: hypothesis testing using phylogenies.
Pond SL, Frost SD, Muse SV
Bioinformatics21p676-9(2005 Mar 1)

PhyML

A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.
Guindon S, Gascuel O
Syst Biol52p696-704(2003 Oct)

ProtTest

ProtTest: selection of best-fit models of protein evolution.
Abascal F, Zardoya R, Posada D
Bioinformatics21p2104-5(2005 May 1)

Also consider citing PhyML and PAL.

PAL

PAL: an object-oriented programming library for molecular evolution and phylogenetics.
Drummond A, Strimmer K
Bioinformatics17p662-3(2001 Jul)

jModelTest

jModelTest: phylogenetic model averaging.
Posada D
Mol Biol Evol25p1253-6(2008 Jul)

Also consider citing PhyML and, if you use jModelTest to build a model-averaged tree, PHYLIP.

RRTree

RRTree: relative-rate tests between groups of sequences on a phylogenetic tree.
Robinson-Rechavi M, Huchon D
Bioinformatics16p296-7(2000 Mar)

SLR

Detecting amino acid sites under positive selection and purifying selection.
Massingham T, Goldman N
Genetics169p1753-62(2005 Mar)

PAML

Codeml

PAML 4: phylogenetic analysis by maximum likelihood.
Yang Z
Mol Biol Evol24p1586-91(2007 Aug)

yn00

Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models.
Yang Z, Nielsen R
Mol Biol Evol17p32-43(2000 Jan)

TrimAl

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T
Bioinformatics25p1972-3(2009 Aug 1)

ETE

ETE: a python Environment for Tree Exploration.
Huerta-Cepas J, Dopazo J, Gabaldón T
BMC Bioinformatics11p24(2010 Jan 13)

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