ViraMiner VS PhaMers

Compare ViraMiner vs PhaMers and see what are their differences.

ViraMiner

CNN based classifier for detecting viral sequences among metagenomic contigs (by NeuroCSUT)
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PhaMers

A bioinformatic tool for identifying bacteriophages using machine learning and k-mers (by jondeaton)
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ViraMiner PhaMers
1 1
28 6
- -
10.0 10.0
over 3 years ago almost 5 years ago
Python Python
- GNU General Public License v3.0 or later
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.

ViraMiner

Posts with mentions or reviews of ViraMiner. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2021-12-18.

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.

What are some alternatives?

When comparing ViraMiner and PhaMers 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

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

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

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

virMine

VirusSeeker-Virome - VirusSeeker is a set of fully automated and modular software package designed for mining sequence data to identify sequences of microbial origin.

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

Cenote_Unlimited_Breadsticks - DEPRECATED: Discover divergent virus sequences, prune flanking cellular sequences, make basic report

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