Rob DeSalle

@ AMNH



software

Random Addition Concatenation Analysis (RADICAL)

Concatenates randomly selected gene partitions and builds phylogenetic trees (MP with PAUP*/ML with RAxML) to examine tree-to-tree agreement of the conconcatenation path. Also calculates ML support per node and partition. See Narechania et al. (2011 Genome Biol Evol).
download    requires Perl, Bioperl, PAUP*, RAxML

In Silico DNA-DNA hybridization (InSiD)

Submitted.
download

Characteristic Attribute Organization System (CAOS)

Identification of diagnostic character states from molecular sequences that have been hierarchically organized (e.g. according to phylogenetic criteria). See Sarkar et al. (2008 Mol Ecol Resources)
download    requires Ruby, BioRuby, BLAST
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Automated Simultaneous Analysis Phylogenetics (ASAP)

Assembles multigene/multispecies alignment matrices and evaluates the relative significance of individual gene partitions within the context of a given phylogenetic hypothesis (in a maximum parsimony context; uses measures such as standard/Partitioned/Hidden Bremer support). See Sarkar et al. (2008 BMC Bioinform)
download    requires Perl, PAUP*

OrthologID

Automates gene orthology determination within a character-based phylogenetic framework. Classifies user-input query sequences into orthologous groups generated from complete genomes. Identifies diagnostic characters defining each orthologous group, as well as diagnostic characters responsible for classifying query sequences. See Chiu et al. (2006 Bioinformatics)
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