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cofold
|
public |
An RNA secondary structure prediction method that takes co-transcriptional folding into account.
|
2024-12-12 |
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nmrglue
|
public |
A module for working with NMR data in Python
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2024-12-12 |
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maxit
|
public |
MAXIT assists in the processing and curation of macromolecular structure data.
|
2024-12-12 |
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abpoa
|
public |
abPOA: fast SIMD-based partial order alignment using adaptive band
|
2024-12-12 |
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trf
|
public |
Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences.
|
2024-12-12 |
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ucsc-countchars
|
public |
Count the number of occurrences of a particular char
|
2024-12-12 |
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vcftools
|
public |
A set of tools written in Perl and C++ for working with VCF files. This package only contains the C++ libraries whereas the package perl-vcftools-vcf contains the perl libraries
|
2024-12-12 |
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seqtk
|
public |
Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format
|
2024-12-12 |
|
ninja-nj
|
public |
Nearly Infinite Neighbor Joining Application
|
2024-12-12 |
|
glnexus
|
public |
scalable gVCF merging and joint variant calling for population sequencing projects.
|
2024-12-12 |
|
scssim
|
public |
A bioinformatics tool for simulating single-cell genome sequencing data
|
2024-12-12 |
|
pbsim3
|
public |
A simulator for all types of Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) long reads
|
2024-12-12 |
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ucsc-wordline
|
public |
chop up words by white space and output them with one
|
2024-12-12 |
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sdust
|
public |
Symmetric DUST for finding low-complexity regions in DNA sequences.
|
2024-12-12 |
|
haploflow
|
public |
Strain-aware viral genome assembler for short read sequence data
|
2024-12-12 |
|
mapcaller
|
public |
MapCaller: combined short-read mapper and variant caller
|
2024-12-12 |
|
ucsc-netsplit
|
public |
Split a genome net file into chromosome net files
|
2024-12-12 |
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ucsc-qacagplift
|
public |
Use AGP to combine per-scaffold qac into per-chrom qac.
|
2024-12-12 |
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fqgrep
|
public |
Search a pair of fastq files for reads that match a given ref or alt sequence
|
2024-12-12 |
|
mergenotcombined
|
public |
Merge Forward and reverse reads from fastq files
|
2024-12-12 |
|
bamhash
|
public |
No Summary
|
2024-12-12 |
|
ucsc-faalign
|
public |
Align two fasta files
|
2024-12-12 |
|
evidencemodeler
|
public |
Evidence Modeler combines ab intio gene predictions, protein alignments, and transcript alignments into weighted consensus gene structures
|
2024-12-12 |
|
booster
|
public |
BOOSTER is a new way of computing bootstrap supports in large phylogenies.
|
2024-12-12 |
|
rustynuc
|
public |
Quick analysis of pileups for likely 8-oxoG locations
|
2024-12-12 |
|
assemblyutility
|
public |
No Summary
|
2024-12-12 |
|
smoothxg
|
public |
Local reconstruction of variation graphs using partial order alignment
|
2024-12-12 |
|
vcfbub
|
public |
Popping bubbles in vg deconstruct VCFs
|
2024-12-12 |
|
ucsc-pslsortacc
|
public |
Remove chain-breaking alignments from chains that break nested chains.
|
2024-12-12 |
|
python-hyphy-python
|
public |
HyPhy package interface library
|
2024-12-12 |
|
fastsimbac
|
public |
Models bacterial recombination
|
2024-12-12 |
|
selam
|
public |
Simulation of Epistasis Local adaptation, with Ancestry and Mate choice
|
2024-12-12 |
|
ucsc-catdir
|
public |
concatenate files in directory to stdout.
|
2024-12-12 |
|
methbat
|
public |
A battery of methylation tools for PacBio HiFi reads
|
2024-12-12 |
|
ucsc-fatotab
|
public |
convert fa file to tab separated file
|
2024-12-12 |
|
ucsc-getrnapred
|
public |
Get virtual RNA for gene predictions
|
2024-12-12 |
|
aprfinder
|
public |
Tool for finding aphased repeats.
|
2024-12-12 |
|
r-loom
|
public |
An interface for the single-cell RNAseq-oriented loom format. Loom files are an HDF5-based format for storing and interacting with large single-cell RNAseq datasets. loomR provides an interface for working with loom files in a loom-specific way; we provide routines for validating loom files, iterating with chunks through data within the loom file, and provide a platform for other packages to build support for loom files.
|
2024-12-12 |
|
ucsc-mafsplit
|
public |
Split multiple alignment files
|
2024-12-12 |
|
snp-dists
|
public |
Convert a FASTA alignment to SNP distance matrix
|
2024-12-12 |
|
aragorn
|
public |
ARAGORN, tRNA (and tmRNA) detection
|
2024-12-12 |
|
rmath4
|
public |
standalone Rmath library from R
|
2024-12-12 |
|
mappy
|
public |
Minimap2 Python binding
|
2024-12-12 |
|
ucsc-pslmap
|
public |
map PSLs alignments to new targets using alignments of
|
2024-12-12 |
|
pin_hic
|
public |
A Hi-C scaffolding method
|
2024-12-12 |
|
ucsc-psltobed
|
public |
transform a psl format file to a bed format file.
|
2024-12-12 |
|
r-soap-nmr
|
public |
No Summary
|
2024-12-12 |
|
ucsc-crtreeindexbed
|
public |
Create an index for a bed file.
|
2024-12-12 |
|
mlrho
|
public |
Takes as input a file with assembled reads from a single diploid individual and returns maximum likelihood estimates of the population mutation rate, , the sequencing error , the zygosity correlation, and the population recombination rate.
|
2024-12-12 |
|
ucsc-bedgeneparts
|
public |
Given a bed, spit out promoter, first exon, or all introns.
|
2024-12-12 |
