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In all analyses, the model of sequence evolution was established using the program Prot-test V. 1.3 [ 56].
Representative proteins and protein families for insertion/deletion analysis were selected based on the protein profile model of the family, established using the program hmmpfam from the HMMER package [ 84].
Differentially bound regions (DBRs) were established using the program MAnorm (Shao et al. 2012), which uses common peaks between two libraries (as called by MACS2) to rescale and normalize ChIP data between two treatments, then estimate significance, direction and magnitude of differential ChIP enrichment for all confident ChIP enrichment peaks.
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46 Before analysis, Mendelian errors were zeroed out using the PEDCHECK program, 47 and basic performance characteristics were established using the PEDSTATS program.
The RIs were established using the RefVal program 4.1b.
Paternity was established using the CERVUS program [ 73].
The identity of these polypeptides was established using the BLAST program available on the NCBI web site.
The true identity of these polypeptides was established using the BLAST program available at the NCBI web site [ 87, 88].
The true identity of these polypeptides was established using the BLAST program [ 34, 35] available at the NCBI web site.
The distribution of amino acid pairs separated by a fixed distance k in a given set of amino acid sequences was established using the simple computer program available from http://lab6.iitp.ru/utils/aapf/.
TNBC subtypes describe by Lehmann and colleagues were established using the online TNBC-type program [ 33].
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