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extract_fullseq
|
public |
extract_fullseq is part of BMTagger aka Best Match Tagger, for removing human reads from metagenomics datasets
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2024-12-11 |
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ucsc-lavtopsl
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public |
Convert blastz lav to psl format
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2024-12-11 |
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filtlong
|
public |
Filtlong is a tool for filtering long reads. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.
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2024-12-11 |
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mgs-canopy
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public |
No Summary
|
2024-12-11 |
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ucsc-bigwigtobedgraph
|
public |
Convert from bigWig to bedGraph format.
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2024-12-11 |
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htsbox
|
public |
HTSbox is a fork of early HTSlib. It is a collection of small experimental tools manipulating HTS-related files.
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2024-12-11 |
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ir
|
public |
Program for Calculating the Repetitiveness of DNA Sequences
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2024-12-11 |
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ucsc-pslliftsubrangeblat
|
public |
lift PSLs from blat subrange alignments
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2024-12-11 |
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ococo
|
public |
Ococo, the first online consensus caller.
|
2024-12-11 |
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potrace
|
public |
A tool for tracing a bitmap, which means, transforming a bitmap into a smooth, scalable image
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2024-12-11 |
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seqyclean
|
public |
Main purpose of this software is to pre-process NGS data in order to prepare for downstream analysis.
|
2024-12-11 |
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slimfastq
|
public |
slimfastq would efficiently compresses/decompresses fastq files
|
2024-12-11 |
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prophex
|
public |
The ProPhex k-mer index.
|
2024-12-11 |
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ucsc-para
|
public |
version 12.18
|
2024-12-11 |
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ucsc-featurebits
|
public |
Correlate tables via bitmap projections.
|
2024-12-11 |
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biolite-tools
|
public |
C++ tools for biolite, a lightweight bioinformatics framework with automated tracking of diagnostics and provenance.
|
2024-12-11 |
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codonw
|
public |
CodonW is a programme designed to simplify the Multivariate analysis (correspondence analysis) of codon and amino acid usage.
|
2024-12-11 |
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lrzip
|
public |
Long Range ZIP or Lzma RZIP. This is a compression program optimised for large files. The larger the file and the more memory you have, the better the compression advantage this will provide, especially once the files are larger than 100MB. The advantage can be chosen to be either size (much smaller than bzip2) or speed (much faster than bzip2).
|
2024-12-11 |
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ucsc-chainnet
|
public |
Make alignment nets out of chains
|
2024-12-11 |
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cyushuffle
|
public |
A Cython wrapper over uShuffle - a useful tool for shuffling biological sequences while preserving the k-let counts
|
2024-12-11 |
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thermorawfileparser
|
public |
Wrapper around the .net (C#) ThermoFisher ThermoRawFileReader library for running on Linux with mono
|
2024-12-11 |
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ltr_finder
|
public |
LTR_Finder is an efficient program for finding full-length LTR retrotranspsons in genome sequences.
|
2024-12-11 |
|
collect_mgf
|
public |
Collects MGF files and dd_results from an XMass setup_QDD.tcl experiment to a single MGF file.
|
2024-12-11 |
|
yaha
|
public |
No Summary
|
2024-12-11 |
|
metacluster
|
public |
No Summary
|
2024-12-11 |
|
phast
|
public |
PHAST is a freely available software package for comparative and evolutionary genomics.
|
2024-12-11 |
|
prefersim
|
public |
PReFerSim is an ANSI C program that performs forward simulations under the PRF model
|
2024-12-11 |
|
ima3
|
public |
IMa3 can be used to solve a fundamental problem in evolutionary genetics, which is to jointly consider phylogenetic history and pouplation genetic history, including gene exchange. IMa3 can be used to estimate the rooted phylogenetic tree for multiple populations, and does so while integrating over all possible Isolation-with-Migration models
|
2024-12-11 |
|
ray
|
public |
No Summary
|
2024-12-11 |
|
ucsc-genepredtofakepsl
|
public |
Create a psl of fake-mRNA aligned to gene-preds from a file or table.
|
2024-12-11 |
|
ucsc-rasqlquery
|
public |
Do a SQL-like query on a RA file.
|
2024-12-11 |
|
strawc
|
public |
Straw bound with pybind11
|
2024-12-11 |
|
geco3
|
public |
An efficient DNA sequence compressor using Neural Networks
|
2024-12-11 |
|
gotohscan
|
public |
a search tool that finds shorter sequences (usually genes) in large database sequences (chromosomes, genomes, ..) by computing all semi-global alignments.
|
2024-12-11 |
|
ucsc-gff3togenepred
|
public |
convert a GFF3 file to a genePred file
|
2024-12-11 |
|
r-hgvsparser
|
public |
hgvsParseR
|
2024-12-11 |
|
lightstringgraph
|
public |
LightStringGraphs (LSG) is an external memory string graph construction tool.
|
2024-12-11 |
|
rust-overlaps
|
public |
A fast and secure command line utilility for enumerating all suffix-prefix
overlaps within a set of sequences, satisfying a user-specified minimal
overlap length and maximal error rate.
|
2024-12-11 |
|
genefuse
|
public |
Gene fusion detection and visualization
|
2024-12-11 |
|
gassst
|
public |
GASSST : Global Alignment Short Sequence Search Tool
|
2024-12-11 |
|
ucsc-sqltoxml
|
public |
dump out all or part of a relational database to XML, guided
|
2024-12-11 |
|
genrich
|
public |
Detecting sites of genomic enrichment.
|
2024-12-11 |
|
pardre
|
public |
ParDRe is a parallel tool to remove duplicate reads.
|
2024-12-11 |
|
clearcut
|
public |
The reference implementation for Relaxed Neighbor Joining (RNJ).
|
2024-12-11 |
|
r-ccube
|
public |
R package for clustering and estimating cancer cell fractions (CCF) of somatic variants (SNVs/SVs) from bulk whole genome/exome data.
|
2024-12-11 |
|
r-disprose
|
public |
Set of tools for molecular probes selection and design of a microarray, e.g. the assessment of physical and chemical properties, blast performance, selection according to sensitivity and selectivity. Methods used in package are described in: Lorenz R., Stephan H.B., Höner zu Siederdissen C. et al. (2011) <doi:10.1186/1748-7188-6-26>; Camacho C., Coulouris G., Avagyan V. et al. (2009) <doi:10.1186/1471-2105-10-421>.
|
2024-12-11 |
|
r-abdiv
|
public |
Alpha and Beta Diversity Measures
|
2024-12-11 |
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ucsc-fafilter
|
public |
Filter fa records, selecting ones that match the specified conditions
|
2024-12-11 |
|
tadarida-d
|
public |
Tadarida-D (Toolbox for Animal Detection on Acoustic Recordings - Detection and Feature extraction part) for Galaxy use.
|
2024-12-11 |
|
autodock
|
public |
AutoDock is a suite of automated docking tools.
|
2024-12-11 |
