Trinity RNA-Seq de novo transcriptome assembly

Automatically exported from code.google.com/p/cdhit

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data

A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data

Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation

Source code of the VirSorter tool, also available as an App on CyVerse/iVirus (https://de.iplantcollaborative.org/de/)

Concatenates FASTA formatted files to one "phyml" (PHYLIP) formatted file

Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to construct a phylogenetic tree. Provides evolutionary analyses (gene…

Escape Excel: a tool for preventing gene symbol and accession conversion errors

A straightforward and complete next-generation sequencing read simulator

SARS-CoV-2 analysis pipeline for multiplex-PCR MPS(Massive Parrallel Sequencing) data

Data and workflow examples

An integrated computational framework for comprehensive transcriptome analyses with Nanopore direct-RNA sequencing data

Perl scripts for manipulating output from phylogenetic MCMC software (MrBayes, BEAST, PhyloBayes, etc)

Whole organelle genome-wide alignment construction method, which ultilizes BLAST tool, to facilitate phylogeny analysis

Easy installation for INSaFLU made by docker

Codes for Highly Pathogenic H5N1, and Swine H1 (Global and US) Clade Classifications

Perl script for manipulating trees after phylogenetic reconstruction

backup for my server

Influenza reassortment detection

Routine utilities for seuqnece operation

Convert output trees from BEAST to other formats

Tips and tricks for your daily life on our servers

Finds changes in amino acid propensities between two species with single-position resolution

AIV_seeker is optimized for detecting and identification of Avian Influenza Virus from metagenomics data.