Pinned

1. treesub treesub Public

   A small program that glues together other programs allowing a user to input a codon alignment in FASTA format and produce an annotated phylogenetic tree showing which substitutions occurred on a gi…

   Java 18 7

2. swmutsel swmutsel Public

   Implementation of the site-wise mutation-selection model (swMutSel) described in Tamuri et al. (2012, 2014) , and Tamuri and dos Reis (2022)

   Java 6 4

3. tdg09 tdg09 Public

   Software and data used in Tamuri AU, dos Reis M, Hay AJ, Goldstein RA (2009) Identifying Changes in Selective Constraints: Host Shifts in Influenza. PLoS Comput Biol 5(11): e1000564 doi:10.1371/jou…

   Java 3 3

4. dng dng Public

   Archschema: graphs of related Pfam domain architectures ("domain network graphs")

   Java 2

5. pal pal Public

   Mirror of Drummond, A., & Strimmer, K. (2001). PAL: an object-oriented programming library for molecular evolution and phylogenetics.

   Java 3

6. tdg12 tdg12 Public

   This program is no longer being updated. Please use the implementation at https://github.com/tamuri/swmutsel

   Java 2