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Sr

Method
name

Latest Free/
version
commercial

Algorithm name

Wed link

Special feature

1.

PHYLIP

3.695

PARSIMONY,DIS
TANCE MATRIX,
LIKELIHOOD

www.evolution.
genetics.washin
gton.edu/phylip
.html

Phylip is a free package
of programs for inferring
phylogenies.It is the
sixth most frequently
cited phylogeny
program.

2.

TREEPUZZLE

5.2

FREE

FREE

LIKELIHOOD
METHOD

www.treepuzzle.de/

References

(10)

tree evaluation, can also
be done for three
sequences.
(11)

Program 4
3.

Mr Bayes

3.2.2

FREE

BAYESIAN
ANALYSIS

www.
mrbayes.source
forge.net

4.

PAUP

4.0

COMMERC
IAL

PARSIMONY

www.Paup.csit.
fsu.edu

Bayesian inference and
model choice across a
wide range of
phylogenetic and
evolutionary model

(12)

It is a standard program
for phylogenetic
analysis.
(13)

This method is based on

REFERENCE: 10.F. Schmidt. Anisimova M. .G. Anisimova M. 59(3):307-21. New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3. Systematic Biology.O. K..0. D. Ackerly. John P. Phylocom:software for the analysis of phylogenetic community structure & trait evolution. Yang. Maddison DR:Interative analysisof phylogeny and character evolution using the computer program MacClade(1989). B.. Vingron. 12. 24:1586-1591 18. Strimmer.Filipski Aand Kumar S (2013) MEGA6:Molecular evolutionary genetics analysis version 6. Gascuel O.0. X.K. New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML .O & evolution.. TREEFINDER: A powerful graphical analysis environment for molecular phylogenetics. 15.Oxford journal.Stecher G. Gascuel. Lefort V.. Tamura K.Molecular biology and evolution 30:2725-2729 21. Gascuel O.53(1-4):190-202 17.M.. 24:2098-2100 19. Dufayard J. Maddison WP. Jobb.Huelsenbeck.A. Tamura K.S.0. DAMBE: Software Package for Data Analysis in Molecular Biology and Evolution. Vol. . Hordijk W. . Desper. 2001 .Z.C.17 no. Felsenstein. 2002. Dufayard J. and Haeseler.Bioinformatics.Stecher G. Hordijk W.F. Bioinformatics.. H. 22.. "Evolutionary trees from DNA sequences: A maximum likelihood approach". 59(3):307-21.A. J. Guindon S.. Xia and Z. 2004 .D & Kembel.Bioinformatics.Petrson D. 14.8 2011 13.Fredrik Ronquist. (1981).Systematic Biology. R... Xie. Haeseler von & Strimmer K. Lefort V.Molecular biology and evolution 30:2725-2729 16. doi:10. 2010. PAML 4: Phylogenetic Analysis by Maximum Likelihood. 2010.O.V.W..1007/BF01734359. 2008.Filipski Aand Kumar S (2013) MEGA6:Molecular evolutionary genetics analysis version 6. Fast and accurate phylogeny reconstruction algorithms based on the minimum evolution principle.. MRBAYES:Bayesian inference of phylogenetic trees. BMC Evolutionary Biology.0. Webb.PMID 7288891 11... 20. Journal of Molecular Evolution 17 (6): 368–376. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. 18:502-504. Guindon S. 3. ..Petrson D.

Bayesian analysis in molecular biology and evolution(BAMBE). Suchand. M. M.*. Lord.D .. BALi-phy: simuntaneously Bayesian inference of of alignment and phylogeny. Ludwig.2005. of Munich. Duquesne university.es> and Theodore Garland. D. version 2. RDP2: recombination detection and analysis from sequence alignments. .. Instituto Miguel Lillo.D.M.V. Husmeier D. Germany . Stamatakis1. 21 (4): 456-463. Beta test v. Diallo. T. MOLPHY version 2. 126-127.P. Bayer M.. * UniFrac: a New Phylogenetic Method for Comparing Microbial Communities+ Author Affiliations 10. Microbiol.doi:10.1093/bioinformatics/btp079 26. 32 (5): 1792-1797. PO. Department of mathematics & computer science. 24. 21 (2): 260-262.Lacey Knowles. Box 8888. H. 2000.A. Goloboff. Milne I. Pablo A.25 no.edu>. Adachi J. James S.2005 Appl. $80. Sci. 29.8228-8235. Meier1 RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees.B.Département d’informatique. of Comput.O 22:2047-2048. Lindner D.ucr. Jr <tgarland@facstaff.7. R.Hasegawa M.. Qc. & Larget B. Vol. .23. Laura S. and Posada2.. Version 1.edu> 31. San Miguel de Tucumán. Leclercq.Williamson1. H3C 3P8. and Makarenkov. Acids Res.C. Bryan C. Oxford journal. 2004 27.B. Ludwig2 and H. T. Bioinformatics 2005.2009. 0. Martin1. Bioinformatics 2005.1128/AEM. 28. A. 25. 35. and Kevin Nixon. Dept. 2003.P. Univ. . Tech. Environ. 71 no. Farris. 12 8228-8235 30. Catherine Lozupone1 and Knight2.71. Bioinformatics 25 (1). . Marshall DF and Wright F (2008).A.J..03 beta. 33. 2004. TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops..2. 32. .Carstens. <tgarland@citrus. Argentina.wisc. and Redelings. Stamatakis. December 2005 vol. Robert C. Phylogenetics. B. Montreal. Downtown Station. Edgar* MUSCLE: multiple sequence alignment with high accuracy and high throughPut Nucl.12. Université du Québec à Montréal. Functions for phylogenetically based statistical analyses Author Ramon Diaz-Uriarte<rdiaz@cnio.0. . D. Wolf. Simon. E . Meier.Kubatko.TNT: Tree Analysis Using New Technology. McGuire G. STEM: species tree estimation using maximumlikelihood for gene trees under coalescence. L.3 Programs for molecular phylogenetics based on maximum likelihood 34.

Marc A.D. A Suchard..doi: 10.M. doi: 10.A.. Diallo. . Philippe Lemey.V. Guindon S. BALi-phy: simuntaneously Bayesian inference of of alignment and phylogeny. Suchand..B. Filip Bielejec. SPREAD:spatial phylogenetic reconstruction of evolutionary dynamics.A. Chevenet F. Bayesian analysis in molecular biology and evolution. and McInerney J. 37. 39.36(Web Server issue):W465-9.F. Nucleic Acids Res. and Larget.. 22:2047-2048.1093/bioinformatics/btm135. TOPD/FMTS: a new software to compare phylogenetic trees.. Phylogenetics.. . 2008 Jul 1..fr: robust phylogenetic analysis for the non-specialist. 23:1556-1558.. Andrew Rambaut. (PubMed) 40. Qc.36. Blanc G. Box 8888. Audic S. Claverie J. 2007. Simon. Leclercq.*.Bioinformatics. 38. Lescot M.. and Makarenkov.03 beta. B. .O. Montreal.B. . 2005.M. Lefort V. Département d’informatique. Downtown Station. Dufayard J. Gascuel O. Puigbo P..D. and Redelings.2000. M. Vol. Duquione University. Guignon V. Epub 2008 Apr 19.*.O. Oxford journal. Garcia-Vallve S.(BAMBE) version 2.20 2011. Phylogeny. Lord. B. . H3C 3P8.1093/bioinformatics/btr 481 41. PO. Université du Québec à Montréal. Dereeper A.27 no. department of mathematics and computer science. .E . Buffet S.