Skip to content

This is a versioned data collection containing a collection of HMMER models to identify the ends of ITS sequences.

Notifications You must be signed in to change notification settings

USDA-ARS-GBRU/ITS_HMMs

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

5 Commits
 
 
 
 

Repository files navigation

DOI

ITS_HMMs

This repository contains HMMER Hidden Markov Models that are used by the program ITSx and ITSXpress to identify the ends on Internal Transcribed Spacer (ITS) regions from eukaryotic genomes.

These models were developed and curated by Henrik Nilsson at the University of Gothenburg.

This repository is an attempt to version the data going forward and record what sets of ITS HMMs were used with each software version

Version 1

  • This is the set of HMM's provided by ITSx 1.1.3 released February 8th, 2021 I do not know how much earlier it was used.
  • HMM version 1 was used by ITSxpress from its initial release until version 2.0.2
  • HMM N is empty

Version 2

5 April 2024

  • New Updates to models A, D, E, F, O, P, R to impove support for oomycetes and fungal taxa with deviant ribosomal genes, notably Wickerhamiella, Calocera, and Mucoromycotina fine root endophytes

  • Addition of Y.hmm to support Parabasalia

About

This is a versioned data collection containing a collection of HMMER models to identify the ends of ITS sequences.

Resources

Stars

Watchers

Forks

Packages

No packages published