matrices | | | |
| MESQUITE |  | Maddison W. P. and D. R. Maddison. 2007. Mesquite: a modular system for evolutionary analysis, v. 2.01. | |
| MACCLADE | | Maddison, D & W. Maddison. MacClade 4.08. | |
| WINCLADA | | Nixon, K. C. 1999. Winclada (BETA) ver. 0.9.9 PUBLISHED BY THE AUTHOR, ITHACA, NY. | |
| arboles | | | |
| TNT | | Goloboff, PA, JS Farris and KC Nixon. 2008. TNT, a free program for phylogenetic analysis. Cladistics 24: 774-786. | |
| PAUP | | Swofford, D. L. 2001. PAUP* Phylogenetic analysis using parsimony (* and other methods), v. 4 beta 10. Sunderland: Sinauer associates. |  |
| PAUPRAT | | Sikes, D. S. and P. O. Lewis. 2001. PAUPRat: PAUP* Implementation of the parsimony ratchet, v. 1 beta software. Storrs: University of Connecticut. | |
| MRBAYES | | Huelsenbeck, J. P. and F. R. Ronquist. 2001. MRBAYES Bayesian inference of phylogeny. Bioinformatics 17: 754-755. | |
| POY | | Varón, A., L. S. Vinh, I. Bomash and W. C. Wheeler. 2007. POY 4.0.0 rc 2398. American Museum of Natural History. | |
secuencias | | | |
| MODELTEST | | Posada, D. and K. A. Crandall. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14: 817-818. mas software relacionado aqui | |
| CLUSTAL | | Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Research 22: 4673-4680. | |
| STATALIGN | | StatAlign is an extendable software package for Bayesian analysis of Protein, DNA and RNA sequences. Multiple alignments, phylogenetic trees and evolutionary parameters are co-estimated in a Markov Chain Monte Carlo framework, allowing for reliable measurement of the accuracy of the results. | |
| SEQSTATE | | Müller, K. 2005. SeqState - primer design and sequence statistics for phylogenetic DNA data sets. Applied Bioinformatics 4: 65-69. | |
| evaluación | | | |
| PRAP | | Müller, K. 2004. PRAP - calculation of Bremer support for large data sets. Molecular Phylogenetics and Evolution 31: 780-782. | |
| TREEROT | | Sorenson, M.D. and E.A. Franzosa. 2007. TreeRot, v. 3. Boston: Boston University. | |
graficos | | | |
PHYUTILITY |
| Smith, S. A. and Dunn, C. W. (2008) Phyutility: a phyloinformatics tool for trees, alignments, and molecular data. Bioinformatics. 24: 715-716 | |
| TREEVIEW X | | Page, R. TreeView X. An open source program to display phylogenetic trees on Linux, Unix, Mac OS X, and Windows platforms. | |
| FIGTREE | | FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. | |
| TREEGRAPH | | Müller and Müller, 2004. | |
| | | | |
| TREEFITTER | | Ronquist, F. TreeFitter Version 1.0 (c) 1999-2001. | |
| TREEMAP | | TREEMAP 1.0 User's Guide Roderic D. M. Page. | |
| PACT | | Wojcicki, M and D. R. Brooks. 2005. PACT: an efficient and powerful algorithm for generating area cladograms.Journal of Biogeography 32:755-774. | |
