The software pipeline is implemented in Python (alignment processing module) and R (statistical analysis module).
The amino acid sequences of the constant exons (see Fig. 2) or the ectodomains 1 3 (EC1-3) (see Fig. 3) of the protocadherin cluster genes from various species were aligned using ClustalW [35] as implemented in BioEdit sequence alignment editor [36] under default parameters.
This method has been implemented in RABEMA (Read Alignment BEnchMArk), a tool that evaluates the result of arbitrary read mappers that support the SAM output format with real and simulated datasets.
Sequences were assembled with CodonCode Aligner [ 34], and aligned with reference HBV sequences from the NCBI nucleotide database [ 35] using ClustalW implemented in BioEdit Sequence Alignment Editor version 7.0.9 [ 36].
Bowtie was implemented in the –v alignment mode with the maximum number of mismatches set to 3. Paired end reads were aligned to the transcriptome with both read pairs needing a valid alignment within a given locus to be counted as a match.
Because use of the IUPAC nomenclature for biallelic SNPs yielded a closer to normal distribution of error than the other methods and was readily implemented in a single alignment strategy, we employed this technique on a transcriptome-wide basis for subsequent analyses.
Deduced amino acid sequences from caspase transcripts retrieved from the various databases searched were aligned together with the Drosophila caspases (Drice, Dcp-1, Decay, Dronc, Dredd, Damm and Strica) and with the C. elegans caspase Ced3 as an outgroup, using the FFT-Ns-i strategy implemented in the MAFFT alignment program [ 71].
The StatAlign package - a Markov chain Monte Carlo (MCMC) sampler implemented in Java - samples alignment parameters, sequence alignments, tree branch lengths and tree topologies in order to infer both the alignment and the phylogenetic tree relating the input sequences [ 28].
The database alignment implemented in Sybyl7.3 [16] was used to align 102 compounds using most active compound 32 as a template.
Sequences were aligned as amino-acid sequences and then back converted to nucleotide sequences (as implemented in SeaView) and alignments were manually checked.
The sequences were first aligned with ClustalW implemented in BioEdit and the alignment was then refined by eye (total 1097 nucleotidic sites, see Suppl. Figure 1) [ 39].
