Software | Version | Type | References | Website |
Alignment information |
2.11 |
Alignment |
Suchard MA and Redelings BD BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny, Bioinformatics, 22:2047-2048, 2006. |
http://www.biomath.ucla.edu/msuchard/bali-phy/ |
BAli-phy |
2.11 |
Alignment |
Suchard MA and Redelings BD BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny, Bioinformatics, 22:2047-2048, 2006. |
http://www.biomath.ucla.edu/msuchard/bali-phy/ |
ClustalW |
1.83 |
Alignment |
Thompson JD, Higgins DG, Gibson TJ.
(1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680. |
http://www.clustal.org/ |
ClustalW2 |
2.1 |
Alignment |
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG.
(2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948. |
http://www.clustal.org/ |
GBlocks |
0.91b |
Alignment |
Talavera, G., and Castresana, J. (2007). Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology 56, 564-577.
Castresana, J. (2000). Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution 17, 540-552. |
http://molevol.cmima.csic.es/castresana/Gblocks.html |
Kalign |
2.03 |
Alignment |
Timo Lassmann and Erik LL Sonnhammer (2005)
Kalign - an accurate and fast multiple sequence alignment algorithm
BMC Bioinformatics 2005, 6:298 doi:10.1186/1471-2105-6-298) |
http://www.ebi.ac.uk/Tools/msa/kalign/ |
Muscle |
3.8.31 |
Alignment |
Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput.Nucleic Acids Res. 32(5):1792-1797.
doi:10.1093/nar/gkh340
Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity BMC Bioinformatics, (5) 113.
doi:10.1186/1471-2105-5-113 |
http://www.drive5.com/muscle/ |
Probcons |
1.12 |
Alignment |
Do CB, Mahabhashyam MS, Brudno M, Batzoglou S (2005) ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res. 15: 330-40. |
http://probcons.stanford.edu/ |
AncestorCC |
1.0 |
Ancestral Reconstruction |
Ancestors 1.0: a web server for ancestral sequence reconstruction.
Diallo AB, Makarenkov V, Blanchette M.
Bioinformatics. 2010 Jan 1;26(1):130-1. Epub 2009 Oct 22.
Exact and heuristic algorithms for the Indel Maximum Likelihood Problem.
Diallo AB, Makarenkov V, Blanchette M.
J Comput Biol. 2007 May;14(4):446-61. |
http://ancestors.bioinfo.uqam.ca/ancestorWeb/ |
Create Local BlastDB |
2.2.25 |
Blast |
BLAST+: architecture and applications.
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL.
BMC Bioinformatics. 2009 Dec 15;10:421 |
http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download |
Local Blast |
2.2.25 |
Blast |
BLAST+: architecture and applications.
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL.
BMC Bioinformatics. 2009 Dec 15;10:421 |
http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download |
jModelTest (Nucleic Acid) |
0.1 |
Evolutionary Model Testing |
Selection of models of DNA evolution with jModelTest.
Posada D.
Methods Mol Biol. 2009;537:93-112. |
http://darwin.uvigo.es/software/jmodeltest.html |
ProtTest (Amino Acid) |
2.4 |
Evolutionary Model Testing |
Abascal F, Zardoya R, Posada, D. 2005. ProtTest: Selection of best-fit models of protein evolution. Bioinformatics: 21(9):2104-2105. |
http://darwin.uvigo.es/software/prottest.html |
HGT Detector 3.2 |
3.2 |
Horizontal Genes Tranfer |
Inferring and validating horizontal gene transfer events using bipartition dissimilarity.
Boc A, Philippe H, Makarenkov V.
Syst Biol. 2010 Mar;59(2):195-211. |
trex.bioinfo.uqam.ca |
LatTrans |
2003 |
Horizontal Genes Tranfer |
Louigi Addario-Berry, Michael T. Hallett, and Jens Lagergren, Towards Identifying Lateral Gene Transfer Events. Pacific Symposium on Biocomputing 2003: 279-290 |
http://www.math.mcgill.ca/louigi/ |
PhyloNet - RiataHGT |
2.4 |
Horizontal Genes Tranfer |
L. Nakhleh, D. Ruths, and L. S. Wang.
RIATA-HGT: A Fast and Accurate Heuristic for Reconstruction Horizontal Gene
Proceedings of the 11th International Computing and Combinatorics Conference (COCOON 05). LNCS #3595 (L. Wang, editor), 84-93. 2005. |
http://bioinfo.cs.rice.edu/phylonet/ |
Random Tree Generator |
|
Random Sequences or Trees |
Kuhner, M., and J. Felsenstein. 1994. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol. Biol. Evol. 11:459-468.
Guindon, S., and O. Gascuel. 2002. Efficient biased estimation of evolutionary distances when substitution rates vary across sites. Mol. Biol. Evol. 19:534-543. |
http://trex.labunix.uqam.ca/index.php?action=randomtreegenerator&project=trex |
Random Tree |
|
Random Sequences or Trees |
(N. Bray and L. Pachter, MAVID: Constrained ancestral alignment of multiple sequences,, Genome Research, 14:693-699 (2004)) |
http://bio.math.berkeley.edu/mavid/ |
Seq-Gen |
1.3.2 |
Random Sequences or Trees |
Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Rambaut A, Grassly NC.
Comput Appl Biosci. 1997 Jun;13(3):235-8. |
http://tree.bio.ed.ac.uk/software/seqgen/ |
PaML (baseml) |
4.4 |
Selective Pressure |
Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24: 1586-1591. |
http://abacus.gene.ucl.ac.uk/software/paml.html |
PaML (codeml) |
4.4 |
Selective Pressure |
Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24: 1586-1591. |
http://abacus.gene.ucl.ac.uk/software/paml.html |
PaML (yn00) |
4.4 |
Selective Pressure |
(A) Nei-Gojobori (1986) method
Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3:418-426
(B) Yang & Nielsen (2000) method
Yang Z, Nielsen R (2000) Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 17:32-43
(C) LWL85, LPB93 & LWLm methods
Li W.-H., C.-I. Wu, Luo (1985) A new method for estimating synonymous and nonsynonymous rates of nucleotide substitutions considering the relative likelihood of nucleotide and codon changes. Mol. Biol. Evol. 2: 150-174.
Li W-H (1993) Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36:96-99
Pamilo P, Bianchi NO (1993) Evolution of the Zfx and Zfy genes - rates and interdependence between the genes. Mol. Biol. Evol. 10:271-281
Yang Z (2006) Computational Molecular Evolution. Oxford University Press, Oxford, England |
http://abacus.gene.ucl.ac.uk/software/paml.html |
Q function |
2011 |
Selective Pressure |
A whole genome study and identification of specific carcinogenic regions of the human papilloma viruses.
Diallo AB, Badescu D, Blanchette M, Makarenkov V.
J Comput Biol. 2009 Oct;16(10):1461-73.
PMID: 19754274 |
|
fastDNAml |
1.2.2 |
Tree |
fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood.
Olsen GJ, Matsuda H, Hagstrom R, Overbeek R.
Comput Appl Biosci. 1994 Feb;10(1):41-8. |
http://iubio.bio.indiana.edu/soft/molbio/evolve/fastdnaml/fastDNAml.html |
Archaeopteryx - Viewer |
0.957 |
Tree |
Han M.V. and Zmasek C.M. (2009). phyloXML: XML for evolutionary biology and comparative genomics. BMC Bioinformatics, 10:356. |
http://www.phylosoft.org/archaeopteryx/ |
Garli |
2.0 |
Tree |
Zwickl, D. J., 2006. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. Ph.D. dissertation,The University of Texas at Austin. |
https://www.nescent.org/wg_garli/Main_Page |
MrBayes |
3.1.2 |
Tree |
MrBayes 3: Bayesian phylogenetic inference under mixed models.
Ronquist F, Huelsenbeck JP.
Bioinformatics. 2003 Aug 12;19(12):1572-4.
Altekar, G., S. Dwarkadas, J. P. Huelsenbeck, and F. Ronquist. 2004. Parallel Metropolis-coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics 20:407-415. |
http://molecularevolution.org/software/phylogenetics/mrbayes |
PhyML |
3.0.1 |
Tree |
"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood." Guindon S, Gascuel O. Systematic Biology. 2003 52(5):696-704.
This is a detailed description of the algorithm. |
http://code.google.com/p/phyml/ |
RootTree (MidPoint) |
|
Tree |
N. Bray and L. Pachter, MAVID: Constrained ancestral alignment of multiple sequences,, Genome Research, 14:693-699 (2004). |
http://bio.math.berkeley.edu/mavid/ |
Scriptree - Viewer |
17 |
Tree |
ScripTree: scripting phylogenetic graphics.
Chevenet F, Croce O, Hebrard M, Christen R, Berry V.
Bioinformatics. 2010 Apr 15;26(8):1125-6. |
http://lamarck.lirmm.fr/scriptree/ |
Robinson&Fould |
|
Tree - Distance |
Robinson, D.R. et L.R. Foulds. (1981). Comparison of phylogenetic trees. Math Biosci., volume 53, pages 131-147. |
trex.bioinfo.uqam.ca |
TreeDist (Phylip) |
3.69 |
Tree - Distance |
Felsenstein, J. 1989. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166. |
http://evolution.genetics.washington.edu/phylip/ |
CONSENSE (Phylip) |
3.69 |
Tree - Phylip |
Felsenstein, J. 1989. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166 |
http://evolution.genetics.washington.edu/phylip.html |
DNADIST (Phylip) |
3.69 |
Tree - Phylip |
Felsenstein, J. 1989. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166. |
http://evolution.genetics.washington.edu/phylip.html |
DNAML (Phylip) |
3.69 |
Tree - Phylip |
Felsenstein, J. 1989. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166. |
http://evolution.genetics.washington.edu/phylip.html |
DNAML-Erate |
1.0 |
Tree - Phylip |
Probabilistic Phylogenetic Inference with Insertions and Deletions.
E. Rivas, S. R. Eddy.
PLoS Comput. Biol., 4:e1000172, 2008. |
http://selab.janelia.org/software.html |
DNAPARS (Phylip) |
3.69 |
Tree - Phylip |
Felsenstein, J. 1989. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166. |
http://evolution.genetics.washington.edu/phylip.html |
NEIGHBOR (Phylip) |
3.69 |
Tree - Phylip |
Felsenstein, J. 1989. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166. |
http://evolution.genetics.washington.edu/phylip.html |
PROTML (Phylip) |
3.69 |
Tree - Phylip |
Felsenstein, J. 1989. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166. |
http://evolution.genetics.washington.edu/phylip.html |
PRODIST (Phylip) |
3.69 |
Tree - Phylip |
Felsenstein, J. 1989. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166. |
http://evolution.genetics.washington.edu/phylip.html |
PROPARS (Phylip) |
3.69 |
Tree - Phylip |
Felsenstein, J. 1989. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166. |
http://evolution.genetics.washington.edu/phylip.html |
RETREE (Phylip) |
3.69 |
Tree - Phylip |
PHYLIP -- Phylogeny Inference Package (Version 3.2).
Felsenstein, J. 1989. Cladistics 5: 164-166 |
http://evolution.genetics.washington.edu/phylip.html |
SEQBOOT (Phylip) |
3.69 |
Tree - Phylip |
Felsenstein, J. 1989. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166. |
http://evolution.genetics.washington.edu/phylip/ |