A phylogeny of the birds of New Zealand

This repository contains supplementary sata associated with this manuscript:

Estimating phylogenies for species assemblages: a complete phylogeny for the past and present native birds of New Zealand
Lanfear R and Bromham L (2011) Molecular Phylogenetics and Evolution 61(3):958–963
http://dx.doi.org/10.1016/j.ympev.2011.07.018

There are four files in this collection:

GeneFinder.py
Python script to search GenBank for sequences that match taxonIDs in a list.
Instructions on use are in the script itself, open the script in a text editor to read them.

SupplementaryData.xls
Contains the species list, taxonomy, the TaxonIDs used for each species, whether the TaxonID is for
the NZ species or a substitute taxon, GenBank accession numbers for each sequence used in the supermatrix
(a -1 indicates that a no data were available for that taxon and that gene), and full details of all
contsraints used ('1' indicates that a given taxon was included in a constraint).

MrBayes_inputfile.nex
An example input file for the MrBayes analysis. Seven of these were run independently.
This file also contains the alignments for each gene.

MrBayes_posterior_sample_trees.nex.zip
The full posterior sample of 133,000 trees from the analysis.
These trees exclude 2,000,000 generations of burnin from each run.

50percent_majorityrule_tree.nex
The 50% majorityrule tree that summarises the full posterior sample of 133,000 trees. This
was calculated by loading each run into MrBayes, and summarising the trees using the 'sumt' command.