PhaMers VS VirusSeeker-Virome

Compare PhaMers vs VirusSeeker-Virome and see what are their differences.

PhaMers

A bioinformatic tool for identifying bacteriophages using machine learning and k-mers (by jondeaton)
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VirusSeeker-Virome

VirusSeeker is a set of fully automated and modular software package designed for mining sequence data to identify sequences of microbial origin. (by guoyanzhao)
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PhaMers VirusSeeker-Virome
1 1
6 16
- -
10.0 10.0
almost 5 years ago over 6 years ago
Python Perl
GNU General Public License v3.0 or later GNU General Public License v3.0 only
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.

PhaMers

Posts with mentions or reviews of PhaMers. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2021-12-18.
  • Bad tools that NEED improvement
    11 projects | /r/bioinformatics | 18 Dec 2021
    PhaMers: several open issues. I opened the one about bad FASTA header parsing. But even when I reformat my headers so that works, new errors pop up (which I didn't bother opening issues for since they were unresponsive to others). Also, output is written to current working directory which is annoying.

VirusSeeker-Virome

Posts with mentions or reviews of VirusSeeker-Virome. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2021-12-18.
  • Bad tools that NEED improvement
    11 projects | /r/bioinformatics | 18 Dec 2021
    VirusSeeker: no installation or running instructions on GitHub. They do have it on their lab website, but you have to edit source files to point to databases. Too much of a pain. So not sure how it works once that is done.

What are some alternatives?

When comparing PhaMers and VirusSeeker-Virome you can also consider the following projects:

metaGEM - :gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

virMine

virnet - VirNet: A deep attention model for viral reads identification

DeePhage - A tool for distinguish temperate phage-derived and virulent phage-derived sequence in metavirome data using deep learning

PPR-Meta - A tool for identifying phages and plasmids from metagenomic fragments using deep learning

MetaRon - Metagenomic opeRon Prediction pipeline. MetaRon presents the first pipeline for the prediction of metagenomic operons without any functional or experimental data.

ViraMiner - CNN based classifier for detecting viral sequences among metagenomic contigs

PhaMers vs metaGEM VirusSeeker-Virome vs virMine PhaMers vs virnet VirusSeeker-Virome vs DeePhage PhaMers vs DeePhage VirusSeeker-Virome vs virnet PhaMers vs virMine VirusSeeker-Virome vs PPR-Meta PhaMers vs MetaRon VirusSeeker-Virome vs metaGEM PhaMers vs ViraMiner VirusSeeker-Virome vs MetaRon