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Trinity RNA-Seq de novo transcriptome assembly
Automatically exported from code.google.com/p/cdhit
Consistent adapter and quality trimming for NGS, 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
LANL-Bioinformatics / PhaME
Forked from sanahmed/PhaMEGiven 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
Codes for Highly Pathogenic H5N1, and Swine H1 (Global and US) Clade Classifications
Perl script for manipulating trees after phylogenetic reconstruction
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.