Just a quick one. In August a nice review paper came out on phylogenetic analysis software: Learning to Become a Tree Hugger | The Scientist. By Amy Maxmen it is a "A guide to free software for constructing and assessing species relationships". Definitely worth checking out.
Among the key links & tools discussed:
- Clustal
- RAxML
- MrBayes
- BEAST
- TNT
- BEAST user group
- FigTree
- Mesquite
- Dendroscope
- Paloverde
- GeoPhylo
- MUSCLE
- MAFFT
- T-Coffee
- SeaView
- Phylogeny.fr
- European Bioinformatics Institute
- CIPRES
- Evolutionary Analysis Mesquite
- Biodiverse
- Bayes Traits
- Lagrange
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