Glass's music can now be recreated in minutes on a music-sequencing package, but it is tremendously hard work to play live.
For phylogenetic reconstruction, sequences were aligned with those of other cardioviruses by using PileUp (Wisconsin Sequence Package, version 11.1; Accelrys, San Diego, CA, USA), and trees were generated with the neighbor-joining method implemented in ClustalX version 1.83 (25 ).
Pairwise sequence alignments and scores were generated using the AllAllDb program of Darwin (Data Analysis and Retrieval With Indexed Nucleotide/peptide sequence package), version 2.0, developed at the ETHZ in Zurich [ 35].
Further annotation and analysis of protein sequence similarities used the Darwin system (Data Analysis and Retrieval With Indexed Nucleotide/peptide sequence package), version 2.0, developed at the ETHZ in Zurich, Switzerland [ 16, 22].
In addition, we would hope to improve SuRFR's flexibility by i) linking it in with other R packages (for example, next-generation sequencing packages and methylation and expression analysis packages), and ii) provide additional utility for user customisation.
Though initially developed for mining DNA sequences, the package RISOTTO can also be used for mining protein sequences.
The sequence alignment was carried out using the Clustal-W multiple sequences alignment package [ 85] implemented in BioEdit 7.0 [ 86] that was then manually adjusted by eye (Additional file 9).
The CLuster Analysis of Sequences (CLANS) software package [ 11] was used to compare all 61 members using BLASTn as described previously [ 3].
The Pregap4 module of the Staden sequence analysis package [ 44] was used to align sequences to determine if the potential SFPs contained sequence polymorphisms.
The Staden sequence analysis package [ 18] was used for sequence assembly and annotation of C. harmani mitogenome.
