New revision Added PAUP. block to log files. Fixed bug with DT criterion. Check the whole revision updates at the wiki. New revision Fixed bug with PAUP. block. Added argument for forwarding standard output to a file. New revision Fixed bug with paths including whitespaces.

PRAP v.2.0b3

Parsimony and likelihood ratchet analyses with PAUP.Functions of PRAP 1. PRAP allows the calculation of Bremer support (BS, Decay values; Bremer 1988) using the parsimony ratchet algorithm (Nixon, 1999). Alternatively, BS can also be computed without

• Category: Miscellaneous
• Developer: bioinfweb.info - Download - Free

Malign v.2.8

The multiple alignment procedures implemented in MALIGN are close parallels to those used to search for minimum length cladograms. The logic and software commands will be clear to those familiar with programs such as Hennig86, NONA, and PAUP.

• Category: Miscellaneous
• Developer: amnh.org - Download - Free

Geneious Basic v.5.6.4

Geneious Basic is a software that speeds up and simplifies research in molecular biology and biochemistry. Geneious is a useful,

• Category: CAD
• Developer: geneious.com - Download - Free

• best bioinformatics software - using software for blast searches on ncbi - sequence alignment - cloning - phylogenetic

MrEnt v.2.2

Draw phylogenetic trees with the help of this program. MrEnt is a software for drawing high-quality, printable phylogenetic trees. It is a user-friendly program that recognizes Nexus tree files (like those generated by e.g.

• Category: Miscellaneous Tools
• Developer: mrent.org - Download - Free

GRate v.1.0

Relative rate tests made easy.

• Category: Miscellaneous
• Developer: bioinfweb.info - Download - Free

DAMBE (Data Analysis and Molecular Biology and Evolution) v.5.2.30

DAMBE (Data Analysis and Molecular Biology and Evolution) help you with data analysis and molecular biology and evolution.Here is a short summary of DAMBE functions 1. Sequence alignment * General sequence alignment with nucleotide and amino acid

• Category: Miscellaneous
• Developer: dambe.bio.uottawa.ca - Download - Free

• paup - phylip - mega - beast - mrbayes

Mesquite v.2.74

Analyze comparative data about organisms fast and easy. Mesquite is program for evolutionary biology, designed to help biologists analyze comparative data about organisms. Its emphasis is on phylogenetic analysis,

• Category: Miscellaneous
• Developer: mesquiteproject.org - Download - Free

BayesTrees v.1.0

View and analyze Bayesian trees with this software. BayesTrees is a software designed to display, analyse and manipulate samples of trees, in particular Bayesian samples.BayesTrees reads files in nexus format. The file must have a translate block,

• Category: Miscellaneous
• Developer: evolution.rdg.ac.uk - Download - Free

Patristic v.1.0

Patristic is a Java software that uses as input different tree files and computes their patristic distances. Patristic allows saving and editing in different ways those distances.

• Category: Miscellaneous
• Developer: bioinformatics.org - Download - Free

• bioinformatics - computational biology - community - research - development

Genie v.3.0

Genie (Genealogy Interval Explorer) is a software for the inference of demographic history from molecular phylogenies. A software for the inference of demographic history from reconstructed molecular phylogenies. It is primarily designed for the

• Category: Miscellaneous
• Developer: evolve.zoo.ox.ac.uk - Download - Free

Geneious PRO x64 v.6.0.4

Geneious Pro is an integrated, cross-platform bioinformatics software suite for manipulating, finding, sharing, and exploring biological data such as DNA sequences or proteins, phylogenies, 3D structure information, publications, etc.

• Category: CAD
• Developer: Biomatters Ltd - Download - Price: $249.00

• molecular biology - biochemistry research - molecular research - bioinformatics - biology

Geneious PRO for Vista v.4.7.6

Geneious Pro is an integrated, cross-platform bioinformatics software suite for manipulating, finding, sharing, and exploring biological data such as DNA sequences or proteins, phylogenies, 3D structure information, publications, etc.

• Category: CAD
• Developer: Biomatters Ltd - Download - Price: $249.00

• molecular biology - biochemistry research - molecular research - bioinformatics - biology

PAUP* (Phylogenetic Analysis Using Parsimony *and other methods) is a computational phylogenetics program for inferring evolutionary trees (phylogenies), written by David L. Swofford. Originally, as the name implies, PAUP only implemented parsimony, but from version 4.0 (when the program became known as PAUP*) it also supports distance matrix and likelihood methods. Version 3.0 ran on Macintosh computers and supported a rich, user-friendly graphical interface. Together with the program MacClade,^[1] with which it shares the NEXUS data format,^[2] PAUP* was the phylogenetic software of choice for many phylogenetists.^[3] Version 4.0 added support for Windows (graphical shell and command line) and Unix (command line only) platforms. However, the graphical user interface for the Macintosh version requires Classic, which is no longer supported by Mac OS X 10.5 and later. There is a command line version of PAUP* for Intel-based Macs. PAUP* is also available as a plugin for Geneious. The program now sports the self-referential title of PAUP* (* Phylogenetic Analysis Using PAUP).

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References[edit]

1. ^D R Maddison & W. P. Maddision (2001-02-08). MacClade 4: Analysis of Phylogeny and Character Evolution. ISBN0-8789-3470-7. Archived from the original on 2011-09-27. Retrieved 2015-12-08.
2. ^Maddison DR, Swofford DJ, Maddison WP (1997). 'NEXUS: an extensible file format for systematic information'. Systematic Biology. 46 (4): 590–621. doi:10.1093/sysbio/46.4.590. ISSN1063-5157. PMID11975335.CS1 maint: uses authors parameter (link)
3. ^Hall, Barry G. (2001). Phylogenetic Trees Made Easy. Sinauer Associates. ISBN0-8789-3311-5.

External links[edit]