The data set, respective alignment length including outgroup, number of sequences in data set excluding outgroup, number of haplotypes excluding outgroup, and number of variable sites excluding outgroup, when gaps are considered missing data, except for the mtDNA data set are given.
Sequence similarity plots are displayed in the LC Bs and the height of the sequence identity plot reflects the average column entropy for the region of the respective alignment.
ALE was then run on each of the respective alignment files to produce likelihood and mapping statistics for each library.
The memory footprint reduction that can be achieved is roughly proportional to the gappyness of the respective alignment.
To prevent loss of 16S pyrotags from the respective alignment schemes, we utilize a merge tool available at http://acai.igb.uiuc.edu/bio/ to merge aligned sequences from both NAST and RDP Infernal into one alignment file.
The tree for Proteobacteria was calculated using the JTT amino acid model [ 44] (-m PROTMIXJTT) and the tree for Bacteria using the WAG model [ 45] (-m PROTMIXWAG), as these models gave the best likelihood scores for a given maximum-parsimony tree of the respective alignments.
For a sample of 50 genes given in Table 3 the presence of recombination in the respective alignments was also manually confirmed using RDP3 [63].
Here, trees are inferred separately from the respective alignments and only relationships appearing in all (or most) of the trees are accepted (see also [ 34]).
In multiple analysis, trees are inferred separately from the respective alignments and only relationships that are well supported in all (or most) of the trees are accepted.
The refined outlier amino acid sequences were reintegrated into the respective MSA using the alignment of the reference species as a backbone.
