#phylo

Scripts for phylogenetics. See the wiki for some workflows.

###Some useful libraries

Biopython: Lots of useful libraries and functions for doing bioinformatics in Python.

p4: Peter Foster's Python package for phylogenetics. Implements complex substitution models, supertree methods, and a lot more.

Gram: Another Peter Foster package. Programmatically draw phylogenetic trees (and in principle other simple vector graphics) with LaTeX and Python.

####Some useful software

#####Phylogenetic trees, phylogenomics, comparative genomics

PhyloBayes: Bayesian trees, implements various mixture models including the author's own CAT and CAT+GTR. Also some molecular dating stuff. Implementations currently faster (fastest? only?) of some of the models. Use the MPI version if at all possible.

IQ-Tree: Very efficient maximum likelihood tree program. Supports fancier models than other ML packages (e.g. profile and matrix mixture models).

ALE: Probabilistic gene tree-species reconciliation methods. Very nice.

#####Sequence alignment, masking MUSCLE: Workhorse sequence aligner, pretty fast.

MAFFT: Flexible sequence aligner, many options depending on size, other properties of the dataset.

Seqtools: Alignment viewer and editor (graphical), among other things.