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assembly_10x

Assembly pipeline for 10X chromium genomes of Mytilus species

easel

Sequence analysis library used by Eddy/Rivas lab code

hmmer

HMMER: biological sequence analysis using profile HMMs

RESCRIPt

REference Sequence annotation and CuRatIon Pipeline

ClipKIT

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

GEMLI

Kilosort

Fast spike sorting with drift correction for up to a thousand channels

MCScanX

MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!

CNEFinder

CNEFinder: Finding Conserved Non-coding Elements in Genomes

synphoni

SYNPHONI is a tool designed for reconstructing the dynamic evolution of syntenic relationships across all scales of phylogenetic distance and genome organization. It thus provides a syntenic complement not only for the last common ancestor of all sample species but for each node of interest within a user-provided cladogram (polytomies accepted). Furthermore, syntenic blocks of extant species are retrieved regardless of whether gene order (collinearity) and gene proximity have been maintained or not.

PanSyn

QDiffusion.jl

Leveraging the full dimensionality of single-cell transcriptomics (among other things!)

HogProf

Phylogenetic profiling with orthology data

cilia_HCI

CellProfiler scripts for analysis of cilia and other cellular components from high throughput confocal imaging

TranscriptomeAssemblyTools

A collection of scripts for processing fastq files in ways to improve de novo transcriptome assemblies, and for evaluating those assemblies.

proch-n50

Perl Module and Utility to calculate N50

N50.sh

bash script to quickly produce some assembly stats

MotionMapper

Sample implementation of the MotionMapper behavioral analysis algorithms

3Dviewer_TrackVisualization

SLHSD

Hybird Scaffolding Tool

Inspector

A tool for evaluate long-read de novo assembly results

goldrush

Linear-time de novo Long Read Assembler

mojo

The Mojo Programming Language

SpCLUST

Spectral Clustering for biological sequences

Identity

ALFATClust

Biological sequence clustering tool with dynamic threshold

treelib

An efficient implementation of tree data structure in python 2/3.

cactus

Official home of genome aligner based upon notion of Cactus graphs

foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.

cellsnake

Cellsnake tool main repo