proSeq Files

ProSeq4 is distributed under GPLv3 licence. 
Source code and binaries for Windows, MacOS and Ubuntu are available: https://sourceforge.net/projects/proseq/
No warranty of any kind is provided - use at your own risk.

ProSeq is a user friendly GUI program to process (open, edit, convert and analyse) DNA sequence data. 
It allows one to open and/or save sequence data in over two dozen file formats (and convert between these formats). It shows sequence alignments in a graphical window and allows the user to edit, manipulate and analyse sequences in various ways. 
Sequence analyses include DNA polymorphism and basic phylogenetic reconstruction (NJ and UPGMA). 
The program can also run coalescent simulations and generate and visualise phylogenies.

Various command line tools are also included for simpler integration into pipelines 
(e.g. vcf2fasta converts vcf to fasta and other formats [msmc2, SelectionHapStats, fastPhase])

The main changes in Proseq4 compared to Proseq3:
- It is now a 64-bit program, which can handle much bigger datasets.
- Much simplified interface that hopefully makes it easier to use.
- PCA analysis helps to explore population structure.
- TreeViewer can now show multiple phylogenies at the same time in a densiTree-like style.
- The trees generated by Coalescent simulations tool can be visualised in treeViewer, which can be useful for teaching.  
- Multiplatform. Compiled versions for Windows, Mac and Linux are available.
- Command line tools to convert files (e.g. convert VCF to fasta with vcf2fasta program) and analyse DNA polymorphism

The program was written for my own work but hopefully others will find it useful…
ProSeq4 was written in Object Pascal with LCL cross-platform library and and can be compiled in "Lazarus FreePascal": https://www.lazarus-ide.org 

Installation:

ProSeq4 (and the earlier versions) comes as a single stand-alone executable binary that does not require installation. Just unzip (or untar on Linux) the downloaded archive and run the executable (proseq4.exe on Windows and ./proseq4 on Linux and macOS). On macOS and Linux you may need to change the mode of the file to executable before running the program: chmod a+x proseq4

Note that both Windows and macOS try to prevent the users downloading and running programs from "unknown" (that is, unregistered with them) source. 
Windows will likely block the download from Sourceforge.net on the basis that it is a "potentially dangerous file", but trying again to download and clicking on "download anyway" usually works. Running proseq4.exe the first time is also blocked by windows, but clicking "run anyway" works. This battle with patronising behaviour of Windows has to be done only for running proseq4 the first time. After that it works ok without any Windows complains about potentially dangerous file.

MacOS allows the user to download the file but then prevents the user from running it. When running proseq4 on a Mac the 1st time you'll likely get the message that the program was created by an unknown developer and cannot be opened, or that the file is damaged and has to be deleted. This error is a false alarm triggered by macOS Gatekeeper, a built-in security feature. When you download an app or a file outside of the official App Store, macOS attaches a hidden "quarantine" tag to it. If the developer hasn't digitally signed or notarized it with Apple, macOS displays this scary warning instead of letting it run. To remove the "quarantine" tag open terminal and go to the folder where the proseq4.app is. Then type 

xattr -cr proseq4.app

This will remove "quarantine" tag and the proseq4 program should run as normal after clicking on proseq4.app in Finder.


Citation:

Filatov D.A. (2024) ProSeq4: A user-friendly multiplatform program for preparation and analysis of large-scale DNA polymorphism datasets. Molecular Ecology Resources, 24:e13962, doi:10.1111/1755-0998.13962

The older versions were published here:

Filatov D.A. (2009) Processing and population genetic analysis of multigenic datasets with ProSeq3 software. Bioinformatics 25(23):3189-90. doi: 10.1093/bioinformatics/btp572.

Filatov D.A (2002) Proseq: A software for preparation and evolutionary analysis of DNA sequence data sets. Molecular Ecology Notes 2 (4), 621-624