The 31 CC-NB-LRR coding nucleotide sequences were aligned with MAFFT [ 75] and checked manually to verify that codon alignment corresponds to amino acid alignment (Additional File 9: Sequence alignment of the coding sequences of RGA08 genes).
We demonstrate through examples how developing distributed systems in Erlang can benefit from BP advantages of incremental development and alignment of the code modules with the requirements.
The protein sequence alignments were then used to construct corresponding alignments of the coding sequences.
Maximum parsimony analyses and maximum parsimony bootstrap support measures were performed with PAUP* v.4.0b10 for Unix [ 59] on the complete alignment with gap coding, as well as the reduced data matrix, with the data sets partitioned into the non-recombined 5' and 3' parts from the GARD recombination detection procedure.
This would include alignment with the union customs code, a common external tariff and an agreement on commercial policy that includes the UK having a say on future EU trade deals.
This alignment determines the coding part together with the reading frame in the EST.
The 960 base-pair sequences represent 40 – 50% of the Hsp70 mRNA, as estimated by alignment with complete coding sequences of mollusc Hsp70s available in GenBank (Pöhlmann et al., in prep).
This fragment and the corresponding part in the other taxa were kept as separate blocks in the final alignment, with the characters of one block coded as missing (see 'Yponomeuta nexus file', Text S1 in the Supplementary Material).
The coding region gap in one of the copies of Hsp70 from D. simulans encompasses the 5' end of the coding region and no alignment with the other Hsp70, including those from D. simulans, is found upstream of this gap.
To obtain final codon alignments, the coding sequences were aligned with PRANK (Löytynoja and Goldman 2005) on the GUIDANCE server (http://guidance.tau.ac.il/; Penn et al. 2010), and the default cutoff of 0.93 confident score was applied for the removal of unreliably aligned positions.
We carried out multiple alignments with the PPR motif coding sequences from the 5 PPR genes from L7rfo and D81Rfo using MUSCLE.
