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Protocols

POPBAM specifications

Information


Unique identifier OMICS_01559
Name POPBAM
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, C++
Computer skills Advanced
Stability Stable
Maintained No

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Publication for POPBAM

POPBAM citations

 (4)
library_books

Intraspecific comparative genomics of isolates of the Norway spruce pathogen (Heterobasidion parviporum) and identification of its potential virulence factors

2018
BMC Genomics
PMCID: 5870257
PMID: 29580224
DOI: 10.1186/s12864-018-4610-4

[…] -MEM.The individual deduplicated BAM files of re-sequenced isolates were merged by SAMtools v.1.2 [] to calculate genome-wide nucleotide diversity and Tajima’s D in non-overlapping 5 Kb windows using PopBam v.3.0 (−m 10, −× 200, −q 40) []. Based on the distribution of D-value, outlier windows (D-value <5th or > 95th percentile) were selected. Genes with at least 80% of their length overlapped in t […]

call_split

The effects of natural selection across molecular pathways in Drosophila melanogaster

2015
BMC Evol Biol
PMCID: 4578789
PMID: 26391223
DOI: 10.1186/s12862-015-0472-4
call_split See protocol

[…] ead data in the NCBI short read archive []. Reads are mapped to the genome of the reference D. melanogaster strain y1;cn1bw1sp1 (version 5.45) using the BWA software []. Variants are called using the POPBAM software with default settings []. Gene alignments are then constructed for the longest transcript per gene from the FlyBase mRNA annotations, using the Perl script PBsnp2fa.pl (https://github. […]

call_split

A New Method to Scan Genomes for Introgression in a Secondary Contact Model

2015
PLoS One
PMCID: 4396994
PMID: 25874895
DOI: 10.1371/journal.pone.0118621
call_split See protocol

[…] resulting alignments for individual lines in the BAM format were merged using the SAMTOOLS software package []. The values of F ST and G min were calculated in non-overlapping 50 kb windows using the POPBAM software package []. We only analyzed nucleotide sites that met the following criteria: read depth per line greater than 5, Phred-scaled scores for the minimum root-mean squared mapping quality […]

library_books

Genome Diversity and Divergence in Drosophila mauritiana: Multiple Signatures of Faster X Evolution

2014
Genome Biol Evol
PMCID: 4202334
PMID: 25193308
DOI: 10.1093/gbe/evu198

[…] Nielsen and colleagues, implemented in the program SweepFinder (), to suggest candidate regions experiencing recent selective sweeps by identifying genomic windows with an unusual SFS. We first used POPBAM to identify all variable sites in the alignment described above. We then focused our analyses on the D. mauritiana lineage by filtering for sites where a derived state was present in at least o […]

Citations

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POPBAM institution(s)
Department of Biology, University of Rochester, Chinahester, NY, USA

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