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)
PhaMers
A bioinformatic tool for identifying bacteriophages using machine learning and k-mers (by jondeaton)
| VirusSeeker-Virome | PhaMers | |
|---|---|---|
| 1 | 1 | |
| 16 | 6 | |
| - | - | |
| 10.0 | 10.0 | |
| over 6 years ago | almost 5 years ago | |
| Perl | Python | |
| GNU General Public License v3.0 only | 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.
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.
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
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.
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
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 VirusSeeker-Virome and PhaMers you can also consider the following projects:
virMine
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