README -- multiple sequence alignments for:

Gordon EL, Kimball RT & Braun EL. Protein structure, models of sequence evolution, and 
data type effects in phylogenetic analyses of mitochondrial data: A case study in birds.

This directory contains eight data files

1)  aa_420taxon_annotated.nex
2)  aa_ExM.phy
3)  aa_TM.phy
4)  aa_combined_ExM_TM.phy
5)  nt_ExM.phy
6)  nt_TM.phy
7)  nt_combined_ExM_TM.nex
8)  nt_combined_ExM_TM.phy
9)  ry_ExM.phy
10) ry_ExM_partition_c123.nex
11) ry_TM.phy
12) ry_TM_partition_c123.nex
13) ry_combined_ExM_TM.phy
14) ry_combined_ExM_TM_partition_c123.nex

They are divided into into amino acid (aa), nucleotide (nt), and binary (ry) files. Note
that the binary files encode the data as 0/1 (A or G = 0; C or T = 1) rather than R and Y

The aa_420taxon_annotated.nex is fully annotated. The phylip file are separated or (when
they are called combined) reassembled so the first set of sites are all ExM followed by a
set of sites that are TM. All of the nt and ry datasets are follow the convention for
phylip files. The partitions for the nt data are included as a sets block along with the
alignments (as a characters block) in the nexus file. For the ry data the partitions are 
in separate nexus file limited to a sets block.

The names are long and they all have the following format:
	Genus_species_ORDER_Family_common_name
	
In all cases they orders correspond to the IOC World Bird list version 6.1
