SrMethod nameLatest versionFree/commercialAlgorithm nameWed linkSpecial featureReferences

1.PHYLIP3.695FREEPARSIMONY,DISTANCE MATRIX, LIKELIHOODwww.evolution.genetics.washington.edu/phylip.htmlPhylip is a free package of programs for inferring phylogenies.It is the sixth most frequently cited phylogeny program. (10)

2.

TREE-PUZZLE 5.2 FREELIKELIHOOD METHODwww.tree-puzzle.de/tree evaluation, can also be done for three sequences. (11)

3.Mr Bayes3.2.2FREEBAYESIAN

ANALYSISwww. mrbayes.source

forge.netProgram 4

Bayesian inference and model choice across a wide range of phylogenetic and evolutionary model (12)

4.PAUP4.0COMMERCIALPARSIMONYwww.Paup.csit.fsu.eduIt is a standard program for phylogenetic analysis. (13)

5.Phyml3.0FREEMAXIMUM LIKELIHOODhttp://www. atgc-montpellier.fr/phyml/.This method is based on maximum likelihood. (14)

6.Tree explorer2.12FREEDISTANCE, MAXIMUM LIKELIHOOD,

PARSIMONYwww.ctu.edu.vn/dvxe/Bioinformatics/software/BIT%20software/TE_man.htmlViews and manipulates MEGA format trees under windows (15)

7.Macclade4.0FREEPARSIMONY ANALYSISwww.macclade.org/macclade.htmlInteractive environment

Exploring phylogeny (16)

8.PAML4.8aFREEMAXIMUM LIKELIHOODabacus.

gene" http://

abacus.

gene.ucl.

ac.uk/

software

/paml.

html.Software used for phylogenetic analysis using maximum likelihood (17)

9.Phylocom4.2FREEDISTANCE BASED METHODPhylodiversity.

net/phylocomSoftware for the analysis of phylogenetic community structure and evolution with phylomatic (18)

10TREE FINDER10.5FREEMAXIMUM LIKELIHOODwww.treefinder.de/Computes phylogenic tree from molecular sequences and infers even large trees by max. likelihood under a variety of models of sequence evolution. It accept both nucleotide and amino acid data and takes rate heterogeneity into account (19)

11MEGA6FREEMAXIMUM LIKELIHOOD, MAXIMUM PARSIMONYhttp://www. megasoftware.net.It is an integrated tool for automatic and maual sequence alignment, inferring phylogenetic trees, mining web-based databases and testing evolutionary hypothesis. (20)

12Fast MECOMMERCIALwww.atgc-montpellier.fr/fastme/Distance method based tool (21)

13DAMBE4.0.36.FREEDISTANCE BASED METHODS, MAXIMUM LIKELIHOOD, PARSIMONYhku.hk/ ~xxia/software/" http://web.

hku.hk/ ~xxia/software/

software.htmData analysis and molecular biology evolution (22)

14RAxMLFREEMAXIMUM LIKELIHOOD

http://wwwbode.cs.tum/~stamatakallows for computation of 1.000-taxon trees in less than 24 hours on a single PC processor (23)

15BEAST1.8COMMERCIALBAYESIAN ANALYSIS beast.bio.ed.ac.ukCross platform program for Bayesian analysis of molecular sequences using MCMC. It is entirely oriented towards rooted, time measured phylogenicsinferred using stick or related molecular models (24)

16STEM1.1FREE MAXIMUM LIKELIHOODStst.osu.edu/~/kubatko/software/STEM/Species tree estimation using maximum likelihood (25)

17RDR24.36http://darwin.

uvigo.es/

rdp/rdp.html (26)

18AxMLMAXIMUM LIKELIHOODFast program for sequential and parallel phylogenetic tree calculation based on maximum likelihood (27)

19MUSCLEFREEhttp://www.

drive5. com/muscle.Multiple sequence alignment with high accuracy and hih thorough point (28)

20UniFrac (29)

21PHYLOGR1.0.6FREEhttp://ligarto.org/rdiaz (30)

22ARB6.0.1FREEPARSIMONY

APPROACHwww.arb-home.deARB graphically oriented package. A central database of orocessed sequence and any additional data is structural according to phylogeny or other defined criteria (31)

23BATWINGNot availableBAYESIAN PARADIGM

(MCMC ALGORITHM)www.mas.ncl.ac.uk/~nijwProgram written in C for analysis of population genetic data, written by Ian Wilson. (32)

24MOLPHY2.363FREEMAXIMUM LIKELIHOODMOLPHY is a free software, and you can use and redistribute it. The programs are written in a standard subset of C with UNIX-like OS. The utilities are written in the "Perl" (Ver.4.036) with UNIX-like OS (33)

25TNT1.0FREEPARSIMONYwww.zmuc.dk/ public/phylogeny/TNT/Program for phylogenetic analysis under parsimony. It incorporatesfast tree searching algorithum (34)

26TOPALi2.5FREEwww.topali.orgProvides phylogenetic model selection, Bayesian analysis, maximum likelihood, phatiolocylogenetic tree estimation, detection of sites under positive selection recombination breakpoint location analysis (35)

27armadillo1.1FREEMAXIMUM LIKELIHOOD,MAXIMUM PARSIMONY AND BAYESIAN ANALYSISwww.bioinfo.uqam.ca/armadillo/Workflow platform dedicated to phylogenetic as well as general bioinformatic analysis (36)

28

BALi- Phy

2.3.5FREE

BAYESIAN

ANALYSISwww.bali-phy.orgBALi-phycanestimate phylogenetic trees from sequences data when the alignment is uncertain(37)

29TOPD/FMTS3.3FREEhttp://genomes.urv.es/topd/TOPD/FMTS is a new software for comparing phylogenetic trees. It has been developed to calculate the differences between trees. The software implements several previously described methods and new algorithms for comparing phylogenetic trees. It combines the TOPD program (TOPological Distance), which compares two trees with the same taxa or two pruned trees, and the FMTS program (From Multiple To Single) (38)

30Phylogeny.fr . http://www.phylogeny.fr/version2_cgi/index.cgiPhylogeny.fr is a free and simple to use web service dedicated to reconstructing and analysing phylogenetic relationships between molecular sequences. Phylogeny.fr runs and connects various bioinformatics programs to reconstruct a robust phylogenetic tree from a set of sequences. (39)

31SPREAD1.0.7BAYESIAN

ANALYSISgithub.com/phylogeography/SPREAD SPREAD is a Java program supporting processing and visualizations of BEASTs phylogeographic models (40)

32BAMBE2.03 betaFREEBAYESIAN

ANALYSIShttp://www.mathcs.duq.edu/larget/bambe.htmlSoftware package for Bayesian analysis of phylogenis. The package include program for analyzing aligned DNA or RNA seq. data and allow data sets with gaps or indeterminate(41)

REFERENCE:

10. Felsenstein, J.(1981). "Evolutionary trees from DNA sequences: A maximum likelihood approach".Journal of Molecular Evolution17(6): 368376.doi:10.1007/BF01734359.PMID728889111.Schmidt, H.A.; Strimmer, K. ; Vingron,M.; and Haeseler,A.V.; TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics. 2002, 18:502-504.

12.John P.Huelsenbeck,Fredrik Ronquist;Bioinformatics;Oxford journal; MRBAYES:Bayesian inference of phylogenetic trees; Vol.17 no.8 201113.Guindon S.; Dufayard J.F.; Lefort V.; Anisimova M.; Hordijk W.; Gascuel O. ; New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML , Systematic Biology, 2010. 3.0. 59(3):307-21.

14. Guindon S., Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O. ;Systematic Biology, New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0. , 2010. 59(3):307-21.

15.Tamura K,Stecher G,Petrson D,Filipski Aand Kumar S (2013) MEGA6:Molecular evolutionary genetics analysis version 6.0.Molecular biology and evolution 30:2725-272916. Maddison WP, Maddison DR:Interative analysisof phylogeny and character evolution using the computer program MacClade(1989);53(1-4):190-20217. Yang,Z. PAML 4: Phylogenetic Analysis by Maximum Likelihood, B.O & evolution. 24:1586-1591

18.Webb,C.O., Ackerly, D.D & Kembel,S.W.; Phylocom:software for the analysis of phylogenetic community structure & trait evolution.Bioinformatics, 2008; 24:2098-2100

19.Jobb,G.K, Haeseler von & Strimmer K. TREEFINDER: A powerful graphical analysis environment for molecular phylogenetics, BMC Evolutionary Biology; 2004 .20. Tamura K,Stecher G,Petrson D,Filipski Aand Kumar S (2013) MEGA6:Molecular evolutionary genetics analysis version 6.0.Molecular biology and evolution 30:2725-272921.Desper. R, Gascuel.O, Fast and accurate phylogeny reconstruction algorithms based on the minimum evolution principle.

22.X. Xia and Z. Xie, DAMBE: Software Package for Data Analysis in Molecular Biology and Evolution, 2001

23.Stamatakis1,*, T. Ludwig2 and H. Meier1 RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 2005. 21 (4): 456-463.

24.Simon,D. & Larget B.; Bayesian analysis in molecular biology and evolution(BAMBE), version 2.03 beta. Department of mathematics & computer science, Duquesne university, 2000.

25. Laura S.Kubatko, Bryan C.Carstens, L.Lacey Knowles; STEM: species tree estimation using maximumlikelihood for gene trees under coalescence; Phylogenetics; Oxford journal; Vol.25 no.7,2009;doi:10.1093/bioinformatics/btp07926.Martin1, D.P. ;Williamson1,C.; and Posada2, D.; RDP2: recombination detection and analysis from sequence alignments, Bioinformatics 2005. 21 (2): 260-262. 2004

27.Stamatakis, A.P. ; Dept. of Comput. Sci., Tech. Univ. of Munich, Germany ; Ludwig, T. ; Meier, H. ; Wolf, M.J.

28.Robert C. Edgar* MUSCLE: multiple sequence alignment with high accuracy and high throughPut Nucl. Acids Res. 2004. 32 (5): 1792-1797.

29.Catherine Lozupone1 and Knight2, R.; * UniFrac: a New Phylogenetic Method for Comparing Microbial Communities+ Author Affiliations 10.1128/AEM.71.12.8228-8235.2005 Appl. Environ. Microbiol. December 2005 vol. 71 no. 12 8228-8235

30.Functions for phylogenetically based statistical analyses Author Ramon Diaz-Uriarte and Theodore Garland, Jr ,

31.Lord, E ; Leclercq,M. ; Diallo,A.B, and Makarenkov,V.,Dpartement dinformatique, Universit du Qubec Montral, PO. Box 8888, Downtown Station, Montreal, Qc, H3C 3P8.

32.Suchand, M.A; and Redelings,B.D ; BALi-phy: simuntaneously Bayesian inference of of alignment and phylogeny.2005. B.O 22:2047-2048.

33.Adachi J.,Hasegawa M; MOLPHY version 2.3 Programs for molecular phylogenetics based on maximum likelihood34.Pablo A. Goloboff, James S. Farris, and Kevin Nixon.TNT: Tree Analysis Using New Technology. Version 1.0, Beta test v. 0.2. Instituto Miguel Lillo, San Miguel de Tucumn, Argentina. $80, 2003.35.Milne I, Lindner D, Bayer M, Husmeier D, McGuire G, Marshall DF and Wright F (2008),TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops, Bioinformatics 25 (1), 126-127.36.Lord,E ; Leclercq,M. ; Diallo,A.B, ; and Makarenkov,V. ; Dpartement dinformatique, Universit du Qubec Montral, PO. Box 8888, Downtown Station, Montreal, Qc, H3C 3P8.

37.Suchand, M.A, and Redelings,B.D, BALi-phy: simuntaneously Bayesian inference of of alignment and phylogeny. B.O, 2005, 22:2047-2048.

38. Puigbo P., Garcia-Vallve S. and McInerney J.O. ; TOPD/FMTS: a new software to compare phylogenetic trees.Bioinformatics, 2007; 23:1556-1558. doi: 10.1093/bioinformatics/btm135.

39. Dereeper A.*, Guignon V.*, Blanc G., Audic S., Buffet S., Chevenet F., Dufayard J.F., Guindon S., Lefort V., Lescot M., Claverie J.M., Gascuel O. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W465-9. Epub 2008 Apr 19. (PubMed)

40. Filip Bielejec, Andrew Rambaut. Marc A. A Suchard, Philippe Lemey; SPREAD:spatial phylogenetic reconstruction of evolutionary dynamics; Phylogenetics; Oxford journal; Vol.27 no.20 2011,doi: 10.1093/bioinformatics/btr 48141.Simon,D. and Larget, B. ; Bayesian analysis in molecular biology and evolution.(BAMBE) version 2.03 beta, department of mathematics and computer science, Duquione University,2000.