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The first two are standard printing formats, PostScript http://www.adobe.com/products/postscript/main.htmland PDF http://www.adobe.com/products/acrobat/adobepdf.html.
Two different multiple alignment programs were then used to align the single read and the genomic sequences: "multalin" http://protein.toulouse.inra.fr/multalin/multalin.htmland "clustalw" http://searchlauncher.bcm.tmc.edu/multi-align/multi-align.html.
Sequences were eventually identified from the Dictyostelium cDNA project in Japan http://www.csm.biol.tsukuba.ac.jp/cDNAproject.htmland the
A second possible approach to library dereplication is to compare sequences against each other using BLAST2 http://www.ncbi.nlm.nih.gov/blast/bl2seq/bl2.htmland then delete duplicates.
The phylogenetic distances between various TMC protein sequences were calculated with ClustalW [ 11 ] http://www.es.embnet.org/Doc/phylodendron/clustal-form.htmland the resulting distance matrix Additional file: 1 (A)was visualized as a tree diagram with centered node position using the Phylodendron phylogenetic tree printer available at http://iubio.bio.indiana.edu/treeapp.