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<br>Lanfear R and Bromham L (2011) Molecular Phylogenetics and Evolution 61(3):958–963<br>http://dx.doi.org/10.1016/j.ympev.2011.07.018 There are four files in this collection: <strong>GeneFinder.py</strong><br>Python script to search GenBank for sequences that match taxonIDs in a list.<br>Instructions on use are in the script itself, open the script in a text editor to read them. <strong>SupplementaryData.xls</strong><br>Contains the species list, taxonomy, the TaxonIDs used for each species, whether the TaxonID is for<br>the NZ species or a substitute taxon, GenBank accession numbers for each sequence used in the supermatrix<br>(a -1 indicates that a no data were available for that taxon and that gene), and full details of all<br>contsraints used ('1' indicates that a given taxon was included in a constraint). <strong>MrBayes_inputfile.nex</strong><br>An example input file for the MrBayes analysis. Seven of these were run independently.<br>This file also contains the alignments for each gene. <strong>MrBayes_posterior_sample_trees.nex.zip</strong><br>The full posterior sample of 133,000 trees from the analysis.<br>These trees exclude 2,000,000 generations of burnin from each run. <strong>50percent_majorityrule_tree.nex</strong><br>The 50% majorityrule tree that summarises the full posterior sample of 133,000 trees. This<br>was calculated by loading each run into MrBayes, and summarising the trees using the 'sumt' command.