Automating Nested Clade Analysis

TCS and GeoDis are the programs to use for NCA, but recently two programs came out that automate NC inference: AUTOINFER and ANeCA.

Addendum (30 Oct 2007)
Panchal & Beaumont (2007) of ANeCA report that Ai-bing Zhang of AUTOINFER has noted that there are some issues in the program that require resolution and that it has temporarily been withdrawn.

Trees: stop fighting!

Tree reconciliation in host-parasite coevolution or in gene-tree fitting has been a long-standing issue in evolutionary biology. Here's some programs that try to bring peace...

TreeMap: for cophylogeny mapping.

TreeFitter: for MP tree-fitting.

SoftParsMap: maps gene trees onto species trees using soft parsimony.

gtp: species tree reconciliation and gene tree parsimony.

UREC: for computing unrooted gene and rooted species tree reconciliation.

CopyCat: easy & fast access to co-phylogenetic analyses. has a wrapper for ParaFit that tests for the association of host and parasite phylogenies.

PriMETV: visualizes tree-within-tree phenomena.

bioinformatics dashboard widgets

Check out ~20 bioinformatics dashboard widgets for OSX Tiger. everything from genetic codes, aminoacid/nucleotide properties, to NCBI BLAST and Entrez. cool!

See the Tree?

Some programs I use to display trees in OSX. Some allow the user to modify trees.

TreeViewX: the industry standard for simple tree visualization.

TreeEdit: views and manipulates trees, re-roots, simulates trees.

FigTree: nice graphical tree viewer.

TreeIllustrator: not only it displays and fiddles with trees, but also has a built-in ToL browser/search engine.

TreeStat: calculates tree statistics (balance, shape, length, popgen).

Phylodendron: draws trees on a webserver or locally (Java app).

TreeJuxtaposer: displays and compares/compresses trees. needs GL4java.

ArboDraw: tree editing with sequence annotation functionality.

TreeMaker: builds taxonomies with species richness data.

TreeSetViz: visualizes tree sets in treespace as a Mesquite module.