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Within 55 individuals we found 25 unique sequence haplotypes for which we produced an alignment spanning 528 characters.
1376 species remain in the alignment, spanning 374 genera, with a total alignment length of 22,612 sites (summarized in Table 1).
The segment (35%) at the top of group F had a dense contiguous alignment spanning the initial 28% of Mt-2.
Reads were retained if a suitable match was found (identity ≥95%, ≥33nt alignment spanning one contig end) and annotated as performed previously (Baillie et al., 2011 ).
We constructed the tree from a gapless region of the NA alignment spanning the entire ThiF domain except for the last two bases.
There are 190 reciprocal indels where a bwa alignment suggests a long Sanger sequencing read alignment spanning a position of a reciprocal deletion (106 of which are in divergent regions).
Similar(44)
The resulting alignment spans 2045 characters.
For all reads where no one alignment spans 90% of the total read length, breseq examines all pairs of alignments reported between the read and the reference genome.
Multiple ClustalW alignment spanned 1080 nucleotides and revealed a high sequence divergence as well as an elevated number of gaps in Catsper1 (see Additional file 2).
All indels identified in the alignment spanned lengths of 3n nucleotides (see Figure 2 and Additional file 2), and thus the reading frame remained intact in all sequences.
The final alignment spanned 3036 bp and was analysed using the default pipeline in SplitsTree4 (UncorrectedP to calculate distances and NeighborNet to build the network).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com