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CHAP specifications


Unique identifier OMICS_21246
Alternative names Cluster History Analysis Package, Chap2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, C++, Python, Shell (Bash)
Computer skills Advanced
Version 2
Stability Stable
Maintained Yes




No version available

CHAP citations


Finding the traces of behavioral and cognitive processes in big data and naturally occurring datasets

Behav Res Methods
PMCID: 5628193
PMID: 28425058
DOI: 10.3758/s13428-017-0874-x

[…] rally occurring data has begun to take hold in cognitive science and psychology (e.g., Goldstone & Lupyan, ; Jones, ), although this focus has a longer tradition in other fields (e.g., economics; see chap. 1 of Davis & Holt, ) and in specific areas of linguistics (e.g., discourse analysis; for a review, see Speer, ). Naturally occurring data sets (NODS) might be called “wild” data, typically gathe […]


AGAPE (Automated Genome Analysis PipelinE) for Pan Genome Analysis of Saccharomyces cerevisiae

PLoS One
PMCID: 4363492
PMID: 25781462
DOI: 10.1371/journal.pone.0120671

[…] ] to find all intervals in each strain that are homologous to the reference genome. Next, for each matching interval we ran a modified version of the annotation utility program included in CHAP2 (The Cluster History Analysis Package). CHAP2 [] uses LASTZ [] for aligning the matching regions to the reference ORF sequences. We used the thoroughly curated SGD reference annotations, and predicted gene […]


Multiple crises and global health: New and necessary frontiers of health politics

PMCID: 3396382
PMID: 22657093
DOI: 10.1080/17441692.2012.691524

[…] air economic arrangements, and bad politics'. The Commission's insistence that reducing health inequities is ‘critically dependent upon changes in the functioning of the global economy’ (, p. 76, and chap. 3, 11 and 15) at first appeared vaguely utopian. Two months later, a financial crisis that spread across the world underscored the importance of this observation, and warnings about the dangers […]


Conversion events in gene clusters

BMC Evol Biol
PMCID: 3161012
PMID: 21798034
DOI: 10.1186/1471-2148-11-226

[…] nverted regions pose the inconvenience of requiring a multiple sequence alignment for each set of homologous sequences. Here, we report the development of an easy-to-use software package called CHAP (Cluster History Analysis Package) for detecting conversion events using gene cluster sequences from multiple species. CHAP uses the conversion-detection method from [], which is based on a statistical […]


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