All ACSL amino acid sequences retrieved in the database mining were initially aligned in MAFFT alignment software using default parameters [ 35] and manually curated with the exclusion of regions of uncertain homology, gaps, and of partial sequences.
More detailed information of used taxa and sequences in each alignment data are summarized in the Additional file 7. To make these alignments, we initially aligned each gene portion by using MUSCLE [ 17] implemented in SeaView ver. 3.2 [ 18].
All statistical analyses were done in R. The 16S rRNA gene sequences of the Bathymodiolus symbionts were imported into the Silva database (release Ref 119) and initially aligned with the SINA aligner (Pruesse et al., 2012).
Raw reads were initially aligned to the full genome using an alignment score of 260 or greater, which for this dataset allowed for only one SNV per read.
For phylogenetic analysis, study sequences and relevant reference sequences were initially aligned with CLUSTALw [ 31] and the alignment was trimmed to a uniform length.
GH32 and RP amino acid sequences from fungal genome data, and the GH32 group 1 nucleotide sequences from genome and experimental data, were initially aligned using MUSCLE [ 41], and the resulting alignments were manually edited.
Sequences were initially aligned using MacClade 4.06 with final editing of the alignments by hand in PAUP* 4.0b10 [ 56], and the alignment was deposited in TreeBase [, accession # S2303].
All sequences were initially aligned with CLUSTAL W 1.83 [ 29] and the preliminary alignments were manually improved in SeaView [ 30].
> -wrap-foot> The 13 PCGs and the two rRNAs were initially aligned with MATTF v6 (Katoh and Toh 2008) and then the alignments were manually optimized.
12S, 16S, and tRNA sequences were initially aligned with Clustal X [ 17] assuming the default pairwise and multiple alignment parameter values.
Mr. Lin initially aligned himself with the revolutionary impulses of the day, but simultaneously probed China's deep past.
