We concatenated all the single-protein alignments into a single 52-protein alignment (8,917 amino acid positions in total), and subjected it to the ML method with the LG + Γ + F model.
We verified that alignments for protein-coding genes were maintained as open-reading frames, and concatenated all individual gene alignments into a single 102,897-bp matrix (derived from 67,506 bp of unaligned plastid sequence data in C. palmata, for reference), including the inverted repeat (IR) regions only once.
For the 500 bp PET libraries sequenced on the HiSeq 2000, we aligned each lane of data in parallel, merged alignments into a single file and inferred fragment size distributions using tools within the ABySS package.
Because mtDNA is inherited as a single unit, we trimmed the ends of each mitochondrial alignment and concatenated alignments into a single file using Mesquite v2.75 [ 41].
If all overlapping transcripts yield consistent gene structures, they are assembled into a single alignment assembly, and by doing so, PASA acts to simply consolidate the transcript alignments into a single gene structure.
Chaining procedure was followed to join the neighbouring local alignments into a single cohesive alignment.
We use a greedy algorithm to integrate the supporting alignments into a single breakpoint call.
Analogously to PSI-BLAST, we use the query as a template for collapsing multiple pairwise alignments into a single MSA and then constructing a corresponding PSSM.
To align such proteins, Kováč et al. [ 16] combined profile HMMs (capturing the properties of the repeating motif) and PHMMs (modeling alignments) into a single scoring scheme that can be decoded by a newly proposed algorithm.
We then aligned the amino acid sequences of individual genes using the MUSCLE plug-in in Geneious Pro v5.5.6 [ 88] with default parameters, and we concatenated all the gene alignments into a single large dataset.
