Recent Package Updates
2025-07-15: bamtools-2.5.3-1 (Tools for BAM alignment files)
Command-line toolkit for reading, writing, and manipulating
BAM (genome alignment) files.
commit log from Hanspeter Niederstrasser ([email protected]):
bamtools: v2.5.32025-07-15: bedtools-2.31.1-1 (Utilities for comparing genomic features)
The BEDTools utilities allow one to address common genomics tasks such as
finding feature overlaps and computing coverage. The utilities are largely
based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.
Using BEDTools, one can develop sophisticated pipelines that answer
complicated research questions by "streaming" several BEDTools together.
The following are examples of common questions that one can address with
BEDTools.
Intersecting two BED files in search of overlapping features.
Culling/refining/computing coverage for BAM alignments based on genome
features.
Merging overlapping features.
Screening for paired-end (PE) overlaps between PE sequences and
existing genomic features.
Calculating the depth and breadth of sequence coverage across defined
"windows" in a genome.
Screening for overlaps between "split" alignments and genomic features.
Quinlan AR and Hall IM, 2010. BEDTools: a flexible suite of utilities for
comparing genomic features. Bioinformatics. 26, 6, pp. 841-842.
commit log from Hanspeter Niederstrasser ([email protected]):
bedtools 2.31.12025-07-15: fasttree-2.2.0-1 (Fast inference of phylogenetic trees)
FastTree infers approximately-maximum-likelihood phylogenetic trees
from alignments of nucleotide or protein sequences. FastTree can handle
alignments with up to a million of sequences in a reasonable amount of
time and memory. For large alignments, FastTree is 100-1,000 times
faster than PhyML 3.0 or RAxML 7.
Price, M.N., Dehal, P.S., and Arkin, A.P. (2009) FastTree: Computing
Large Minimum-Evolution Trees with Profiles instead of a Distance
Matrix. Molecular Biology and Evolution 26:1641-1650,
doi:10.1093/molbev/msp077.
commit log from Hanspeter Niederstrasser ([email protected]):
fasttree: v2.2.02025-07-15: bcftools-1.22-1 (Tools for VCF/BCF files)
BCFtools is a set of utilities that manipulate variant calls in the
Variant Call Format (VCF) and its binary counterpart BCF. All commands
work transparently with both VCFs and BCFs, both uncompressed and
BGZF-compressed.
Most commands accept VCF, bgzipped VCF and BCF with filetype detected
automatically even when streaming from a pipe. Indexed VCF and BCF will
work in all situations. Un-indexed VCF and BCF and streams will work in
most, but not all situations. In general, whenever multiple VCFs are
read simultaneously, they must be indexed and therefore also compressed.
BCFtools is designed to work on a stream. It regards an input file "-"
as the standard input (stdin) and outputs to the standard output
(stdout). Several commands can thus be combined with Unix pipes.
commit log from Hanspeter Niederstrasser ([email protected]):
bcftools: 1.222025-07-15: muscle-5.3-2 (Protein multiple sequence alignment software)
MUSCLE is public domain multiple alignment software for protein and
nucleotide sequences. MUSCLE stands for multiple sequence comparison
by log-expectation.
R.C. Edgar (2021) "MUSCLE v5 enables improved estimates of phylogenetic
tree confidence by ensemble bootstrapping"
https://www.biorxiv.org/content/10.1101/2021.06.20.449169v1.full.pdf
commit log from Hanspeter Niederstrasser ([email protected]):
muscle: v5.32025-07-15: rdp-classifier-2.14-1 (Bayesian classifier of taxonomic data)
The RDP Classifier is a naive Bayesian classifier which was developed to
provide rapid taxonomic placement based on rRNA sequence data. The RDP
Classifier can rapidly and accurately classify bacterial 16s rRNA sequences
into the new higher-order taxonomy proposed by Bergey's Trust. It provides
taxonomic assignments from domain to genus, with confidence estimates for
each assignment. The RDP Classifier is not limited to using the bacterial
taxonomy proposed by the Bergey's Manual. It worked equally well when trained
on the NCBI taxonomy. The RDP Classifier likely can be adapted to additional
phylogenetically coherent bacterial taxonomies. The new updated RDP Classifier
now works on Fungal LSU sequences.
Wang, Q, G. M. Garrity, J. M. Tiedje, and J. R. Cole. 2007. Naive
Bayesian Classifier for Rapid Assignment of rRNA Sequences into the
New Bacterial Taxonomy. Appl Environ Microbiol. 73(16):5261-7;
doi: 10.1128/AEM.00062-07 [PMID: 17586664]
commit log from Hanspeter Niederstrasser ([email protected]):
rdp-classifier: v2.142025-07-15: mothur-1.48.3-1 (Microbial ecology software suite)
Microbial ecology software suite
commit log from Hanspeter Niederstrasser ([email protected]):
mothur: v1.48.32025-07-15: samtools-1.22-1 (Tools for SAM alignment files)
SAM Tools provide various utilities for manipulating alignments in
the SAM format, including sorting, merging, indexing and generating
alignments in a per-position format.
commit log from Hanspeter Niederstrasser ([email protected]):
samtools 1.222025-07-15: vcftools-0.1.17-1 (Tools for VCF files)
Program package designed for working with VCF files, such as
those generated by the 1000 Genomes Project. The aim of VCFtools
is to provide methods for working with VCF files: validating,
merging, comparing and calculate some basic population genetic
statistics.
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, et al.
The variant call format and VCFtools. Bioinformatics. 2011;27(15):2156-8.
Epub 2011/06/10. doi: 10.1093/bioinformatics/btr330. PubMed PMID:
21653522; PubMed Central PMCID: PMC3137218.
commit log from Hanspeter Niederstrasser ([email protected]):
vcftools: 0.1.172025-07-15: libhts3-shlibs-1.22-1 (Library for high-throughput sequencing data)
HTSlib is an implementation of a unified C library for accessing common
file formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput
sequencing data. It is the core library used by samtools and bcftools.
HTSlib: C library for reading/writing high-throughput sequencing data
James K Bonfield, John Marshall, Petr Danecek, Heng Li, Valeriu Ohan,
Andrew Whitwham, Thomas Keane, Robert M Davies GigaScience, Volume 10,
Issue 2, February 2021, giab007,
https://doi.org/10.1093/gigascience/giab007
commit log from Hanspeter Niederstrasser ([email protected]):
libhts3: v1.222025-07-15: libstaden-read11-shlibs-1.14.9-2 (Library for reading/writing DNA seq. results)
A fully developed set of DNA sequence assembly (Gap4 and Gap5),
editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.
commit log from Hanspeter Niederstrasser ([email protected]):
libstaden-read: add packaging notes
