synteny update to python3 (but the code looks fishy, the -synteny option now gets a deprecated warning)
proteinortho now only print html for <10 files automatically and otherwise only gives the option
4. Nov (uid: 4020)
FIXED: sometimes the python3 version produces one edditional edge (global defintion of ALPHA). Special thanks for this update goes to Daniel Doerr for fixing this.
25. Nov (uid: 4030)
added proteinortho_history
the synteny option ffadj is now not depricated anymore
10. Dec (uid: 4196)
improved proteinortho_history
removed the new diamond spam
+ added proteinortho_summary.pl for a summary of proteinortho-graph on species level.
Proteinortho is a tool to detect orthologous genes within different species. For doing so, it compares similarities of given gene sequences and clusters them to find significant groups. The algorithm was designed to handle large-scale data and can be applied to hundreds of species at one. Details can be found in <ahref="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-124">Lechner et al., BMC Bioinformatics. 2011 Apr 28;12:124.</a>
To enhance the prediction accuracy, the relative order of genes (synteny) can be used as additional feature for the discrimination of orthologs. The corresponding extension, namely PoFF (doi:10.1371/journal.pone.0105015), is already build in Proteinortho. The general workflow of proteinortho is depicted [].
Proteinortho is a tool to detect orthologous genes within different species.
# New Features of Proteinortho Version 6!
For doing so, it compares similarities of given gene sequences and clusters them to find significant groups.
The algorithm was designed to handle large-scale data and can be applied to hundreds of species at one.
Details can be found in ([doi:10.1186/1471-2105-12-124](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-124)).
To enhance the prediction accuracy, the relative order of genes (synteny) can be used as additional feature for the discrimination of orthologs. The corresponding extension, namely PoFF ([doi:10.1371/journal.pone.0105015](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0105015)), is already build in Proteinortho. The general workflow of proteinortho:
Input: multiple fasta files (orange box) with many proteins/genes (circles).
First an initial all vs. all comparison between all proteins of all species is performed to determine protein similarities (upper right image).
The second stage is the clustering of similar genes to meaningful co-orthologous groups (lower right image). Connected components within this graph can be considered as putative co-orthologous groups in theory and are returned in the output (lower left image).
# New Features of Proteinortho Version 6
- Implementation of various Blast alternatives for step (for -step=2 the -p= options): Diamond, MMseqs2, Last, Topaz, Rapsearch2, Blat, Ublast and Usearch
- Multithreading support for the clustering step (-step=3)
- Integration of the LAPACK Fortran Library for a faster clustering step (-step=3)
- Integration of the bitscore weights in the connectivity calculation for more data dependant splits (-step=3)
<summary>Minor features: (Click to expand)</summary>
<summary>Minor new features: (Click to expand)</summary>
- Output now supports OrthoXML (-xml) and HTML.
-[proteinortho_history.pl](https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Tools%20and%20additional%20programs) a new tool for tracking proteins (or pairs of proteins) in the workflow of proteinortho.
- New heuristics for connectivity calculation (-step=3).
</details>
<details>
<summary>6.0.12: (Click to expand)</summary>
- removed the diamond spam
- improved [proteinortho_history.pl](https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Tools%20and%20additional%20programs) : now the program is "smarter" in detecting files automatically
- added [proteinortho_summary.pl](https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Tools%20and%20additional%20programs) : a tool for summarizing the proteinortho-graph on species level. With the output it is easy to identify weak connected species.
</details>
# Continuous Integration
supports
The badge
[](https://gitlab.com/paulklemm_PHD/proteinortho/commits/master) indicates the current status of the continuous integration (CI) among various platforms (ubuntu, centos, debian, fedora) and GNU c++ versions (5, 6, latest)
The whole git repository gets deployed on a clean docker imager (gcc:latest,gcc:5,ubuntu:latest,fedora:latest,debian:latest,centos:latest) and compiled (make all) and tested (make test). The badge is green only if all test are passed. For more information see [Continuous Integration (proteinortho wiki)](https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Continuous%20Integration).
A more detailed list of all changes: [CHANGELOG](https://gitlab.com/paulklemm_PHD/proteinortho/blob/master/CHANGELOG)
# Table of Contents
1.[Installation](#installation)
@@ -30,12 +48,18 @@ The whole git repository gets deployed on a clean docker imager (gcc:latest,gcc:
4.[PoFF synteny extension](#poff)
5.[Output description](#output)
6.[Examples](#examples)
7.[Error Codes and Troubleshooting](https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error-Codes) <- look here if you cannot compile/run (proteinortho wiki)
8.[Large compute jobs example](https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Large-compute-jobs-(the--jobs-option)) (proteinortho wiki)
Bug reports: See chapter 7. or send a mail to incoming+paulklemm-phd-proteinortho-7278443-issue-@incoming.gitlab.com (Please include the 'Parameter-vector' that is printed for all errors)
You can also send a mail to lechner@staff.uni-marburg.de.
# [Proteinortho-Wiki](https://gitlab.com/paulklemm_PHD/proteinortho/wikis/) Table of Contents
1.[Tools and additional programs](https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Tools%20and%20additional%20programs)
2.[Error Codes and Troubleshooting](https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error-Codes) <- look here if you cannot compile/run proteinortho
3.[Large compute jobs example](https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Large-compute-jobs-(the--jobs-option))
Bug reports: Please have a look at chapter [2.](https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error-Codes) first or send a mail to incoming+paulklemm-phd-proteinortho-7278443-issue-@incoming.gitlab.com. (please include the 'parameter-vector' that is printed for all errors)
You can also send mails to lechner@staff.uni-marburg.de. Any suggestions, feedback and comments are welcome!
# Installation
@@ -88,7 +112,7 @@ Afterwards the deb package can be installed with `sudo dpkg -i proteinortho*deb`
<br>
#### 1. Prerequisites
#### Prerequisites for compiling proteinortho from source
Proteinortho uses standard software which is often installed already or is part of then package repositories and can thus easily be installed. The sources come with a precompiled version of Proteinortho for 64bit Linux.
@@ -126,7 +150,7 @@ Proteinortho uses standard software which is often installed already or is part
<br>
#### 2. Building and installing proteinortho from source (linux and osx)
#### Building and installing proteinortho from source (linux and osx)
Here you can use a working lapack library, check this with 'dpkg --get-selections | grep lapack'. Install lapack e.g. with 'apt-get install libatlas3-base' or liblapack3.
@@ -179,7 +203,7 @@ OR(!) specify the new g++ in 'make CXX=/usr/local/bin/g++-7 all'
[100%] Everything is compiled with no errors.
</pre>
The compilation of proteinortho_clustering has multiple fall-back routines. If everything fails please look here [Troubleshooting (proteinortho wiki)](https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Codes).
The compilation of proteinortho\_clustering has multiple fall-back routines. If everything fails please look here [Troubleshooting (proteinortho wiki)](https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Codes).
</details>
@@ -214,21 +238,13 @@ If you have problems compiling/running the program go to [Troubleshooting (prote
<br>
# SYNOPSIS
> **proteinortho6.pl [options] \<fasta file(s)\>** (one fasta for each species, at least 2)
OR
> **proteinortho [options] \<fasta file(s)\>**
one fasta for each species; at least 2
# DESCRIPTION
**proteinortho** is a tool to detect orthologous genes within different
species. For doing so, it compares similarities of given gene sequences
and clusters them to find significant groups. The algorithm was designed
to handle large-scale data and can be applied to hundreds of species at
one. Details can be found in Lechner et al., BMC Bioinformatics. 2011 Apr
28;12:124. To enhance the prediction accuracy, the relative order of genes
(synteny) can be used as additional feature for the discrimination of
orthologs. The corresponding extension, namely PoFF (doi:10.1371/journal.pone.0105015), is already build in Proteinortho.
species.
Proteinortho assumes, that you have all your gene sequences in FASTA
format either represented as amino acids or as nucleotides. The source
@@ -302,6 +318,7 @@ Open `proteinorthoHelper.html` in your favorite browser or visit [lechnerlab.de/
- diamond : Only for protein files! standard diamond procedure and for
genes/proteins of length >40 with the additional --sensitive flag
Warning: Please use version 0.9.29 or later to avoid this known bug: https://gitlab.com/paulklemm_PHD/proteinortho/issues/24
- lastn,lastp : lastal. -n : dna files, -p protein files (BLOSUM62
scoring matrix)!
@@ -343,7 +360,6 @@ Open `proteinorthoHelper.html` in your favorite browser or visit [lechnerlab.de/
