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kalign2
|
public |
Kalign is a fast and accurate multiple sequence alignment algorithm designed to align large numbers of protein sequences.
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2024-12-13 |
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gvcfgenotyper
|
public |
A utility for merging and genotyping Illumina-style GVCFs.
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2024-12-13 |
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perl-acme-damn
|
public |
'Unbless' Perl objects.
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2024-12-13 |
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r-lme4qtl
|
public |
Linear mixed models (lme4) with flexible covariance structure for qtl and association analysis.
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2024-12-13 |
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pizzly
|
public |
Fast fusion detection using kallisto
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2024-12-13 |
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starcode
|
public |
Starcode: sequence clustering based on all-pairs search
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2024-12-13 |
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nanoblaster
|
public |
Basic Local Alignment and Search Tool for Oxford Nanopore Long Sequences
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2024-12-13 |
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genometester4
|
public |
A toolkit for performing set operations - union, intersection and complement - on k-mer lists.
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2024-12-13 |
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ucsc-hgspeciesrna
|
public |
Create fasta file with RNA from one species
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2024-12-13 |
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dialign2
|
public |
DIALIGN multiple sequence alignment using various sources of external information
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2024-12-13 |
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perl-gdtextutil
|
public |
Text utilities for use with GD
|
2024-12-13 |
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ucsc-trfbig
|
public |
Mask tandem repeats on a big sequence file.
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2024-12-13 |
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ucsc-bedgraphtobigwig
|
public |
Convert a bedGraph file to bigWig format.
|
2024-12-13 |
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fqzcomp
|
public |
Fqzcomp is a basic fastq compressor, designed primarily for high performance.
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2024-12-13 |
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ucsc-maffrag
|
public |
Extract maf sequences for a region from database
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2024-12-13 |
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epa-ng
|
public |
Massively parallel phylogenetic placement of genetic sequences
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2024-12-13 |
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btrim
|
public |
This tool is made to remove "tips" (short dead ends) from a compacted de Bruijn graph and more generally to remove sequencing errors. Used in Bcool a short read corrector (https://arxiv.org/abs/1711.03336)
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2024-12-13 |
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ucsc-genepredtomafframes
|
public |
create mafFrames tables from a genePreds
|
2024-12-13 |
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ucsc-maffilter
|
public |
Filter out maf files. Output goes to standard out
|
2024-12-13 |
|
r-annotables
|
public |
Provides tables for converting and annotating Ensembl Gene IDs.
|
2024-12-13 |
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ucsc-pslrecalcmatch
|
public |
Recalculate match,mismatch,repMatch columns in psl file.
|
2024-12-13 |
|
ucsc-axtchain
|
public |
Chain together axt alignments.
|
2024-12-13 |
|
ucsc-parasol
|
public |
Parasol is the name given to the overall system for managing jobs on a computer cluster and to this specific command. This command is intended primarily for system administrators. The 'para' command is the primary command for users.
|
2024-12-13 |
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ucsc-twobitmask
|
public |
apply masking to a .2bit file, creating a new .2bit file
|
2024-12-13 |
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ucsc-facount
|
public |
count base statistics and CpGs in FA files.
|
2024-12-13 |
|
bcov
|
public |
BCov is a software package designed for predicting protein beta-sheet topology from amino acid sequence.
|
2024-12-13 |
|
ucsc-mafgene
|
public |
output protein alignments using maf and genePred
|
2024-12-13 |
|
twopaco
|
public |
A fast constructor of the compressed de Bruijn graph from many genomes.
|
2024-12-13 |
|
ntcard
|
public |
Estimating k-mer coverage histogram of genomics data
|
2024-12-13 |
|
ucsc-chaintopsl
|
public |
Convert chain file to psl format
|
2024-12-13 |
|
perl-unicode-utf8
|
public |
Encoding and decoding of UTF-8 encoding form
|
2024-12-13 |
|
lambda
|
public |
Lambda is a local aligner optimized for many query sequences and searches in protein space
|
2024-12-13 |
|
ucsc-bedcommonregions
|
public |
Create a bed file (just bed3) that contains the regions common to all inputs.
|
2024-12-13 |
|
ucsc-genepredcheck
|
public |
validate genePred files or tables
|
2024-12-13 |
|
ucsc-paranode
|
public |
version 12.18
|
2024-12-13 |
|
fpa
|
public |
Filter Pairwise Alignment filter long read mapping information to save disk space
|
2024-12-13 |
|
mason
|
public |
Mason is a collection of tools for the simulation of biological sequences.
|
2024-12-13 |
|
ucsc-maftobigmaf
|
public |
Put ucsc standard maf file into bigMaf format
|
2024-12-13 |
|
bxtools
|
public |
Tools for analyzing 10X Genomics data
|
2024-12-13 |
|
stereogene
|
public |
StereoGene: Rapid Estimation of Genomewide Correlation of Continuous or Interval Feature Data
|
2024-12-13 |
|
plink2
|
public |
Whole genome association analysis toolset
|
2024-12-13 |
|
ucsc-axttopsl
|
public |
Convert axt to psl format
|
2024-12-13 |
|
ucsc-fanoise
|
public |
Add noise to .fa file
|
2024-12-13 |
|
ucsc-htmlcheck
|
public |
Do a little reading and verification of html file
|
2024-12-13 |
|
comparems2
|
public |
A simple tool developed to compare, globally, all MS/MS spectra between two datasets (in Mascot Generic Format or MGF).
|
2024-12-13 |
|
migrate-n
|
public |
Population Genetics - Panmixia and Migration detection
|
2024-12-13 |
|
strike
|
public |
A program to evaluate protein multiple sequence alignments using a single protein structure.
|
2024-12-13 |
|
fastspar
|
public |
Rapid and scalable correlation estimation for compositional data
|
2024-12-13 |
|
ucsc-texthistogram
|
public |
Make a histogram in ascii
|
2024-12-13 |
|
hcluster_sg
|
public |
A tool for hierarchically clustering on a sparse graph
|
2024-12-13 |
