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bx-python specifications


Unique identifier OMICS_18239
Name bx-python
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes




No version available


  • person_outline James Taylor

bx-python citations


Transcriptional Variation of Diverse Enteropathogenic Escherichia coli Isolates under Virulence Inducing Conditions

PMCID: 5527300
DOI: 10.1128/mSystems.00024-17

[…] y sequenced E. coli and Shigella genomes by whole-genome phylogenomic analysis as previously described (, ). The genomes were aligned using Mugsy (), and homologous blocks were concatenated using the bx-python toolkit (https://bitbucket.org/james_taylor/bx-python). The columns that contained one or more gaps were removed using Mothur (). The resulting 1.98-Mb aligned region from each of the genome […]


Evolutionary re wiring of p63 and the epigenomic regulatory landscape in keratinocytes and its potential implications on species specific gene expression and phenotypes

Nucleic Acids Res
PMCID: 5737389
PMID: 28505376
DOI: 10.1093/nar/gkx416
call_split See protocol

[…] hg19/vsMm10/reciprocalBest/). Two different software programs were used to process these alignments and find homologous regions to mouse p63 targets: UCSC liftover tool and bnMapper () implemented in bx-python (More details: https://bitbucket.org/james_taylor/bx-python/wiki/bnMapper). Similar analysis was also repeated in reverse, to map the 25 920 p63 bound genomic targets in human to homologous […]


Epigenetic and genetic alterations and their influence on gene regulation in chronic lymphocytic leukemia

BMC Genomics
PMCID: 5353786
PMID: 28302063
DOI: 10.1186/s12864-017-3617-6

[…] To map genomic regions (i.e., dREs, sREs and hiMRs) from the human to the mouse genome, we used the software “bnMapper” (available at https://bitbucket.org/james_taylor/bx-python/wiki/bnMapper). The pair-wise genome alignment (chain file) between the mouse and human required by bnMapper was downloaded from the UCSC Genome browser. bnMapper was run with the setting “- […]


Inter population Differences in Retrogene Loss and Expression in Humans

PLoS Genet
PMCID: 4608704
PMID: 26474060
DOI: 10.1371/journal.pgen.1005579

[…] ] whole genome alignment from Ensembl release 73 [], requiring a reciprocal overlap of at least 50% between retrocopy sequences from different organisms in the alignment. To be more specific, we used bx-python package to extract genome alignment blocks corresponding to retrocopies annotated in RetrogeneDB. BEDtools [] software was then used to find sets of overlapping blocks that constituted ortho […]


Sequence variants from whole genome sequencing a large group of Icelanders

Sci Data
PMCID: 4413226
PMID: 25977816
DOI: 10.1038/sdata.2015.11

[…] he Ensembl Compara API was used to convert the Compara EMF files storing the multiple alignments to MAF format. For polarization of indels, ancestral sequences were retrieved from the MAF files using bx-python.Ancestral states of SNPs were inferred by comparison with the FASTA sequence for the Ensembl Compara human ancestor sequence for Homo sapiens (GRCh37).When infering the ancestral state of an […]


Genome wide comparative analysis reveals human mouse regulatory landscape and evolution

BMC Genomics
PMCID: 4333152
PMID: 25765714
DOI: 10.1186/s12864-015-1245-6

[…] ChIP-Seq TFos and DHSs can be downloaded from the Mouse ENCODE web portal http://mouse.encodedcc.org/data and http://www.mouseencode.org/.The mapping software can be freely downloaded as part of the bx-python software library from https://bitbucket.org/james_taylor/bx-python/wiki/Home.Ensembl EPO 12-way alignments version 65 can be downloaded from the Ensembl (December 2011) at ftp://ftp.ensembl. […]

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