Please note

This software is posted here so it can be available to those who might find it useful. The project was hosted at taylor0 for many years, but given that I graduated from UCLA and moved from that lab over 10 years ago, it seems like a good time to host it elsewhere for archival purposes. The site below is a rough copy of the latest version from 2008. Not all links may work, but you should be able reach the downloads. Good luck!

TL;DR: Download from SourceForge; Paper describing Formatomatic (citation)
NC Manoukis
3 Sep 2018.

Formatomatic: Population Genetic File Creator and Converter

Current Version

Current version is 0.8.1 (yummy bugfix!), released 14 May 2008 by Nick Manoukis.

Introduction

Formatomatic creates infiles for several population genetic analysis programs from csv, genepop or convert* (excel) files. It only handles diploid microsatellite data for now. I may eventually include other read or write formats (email me if there is some functionality you need and I will work on it if I have time).

This program was initially developed for in-lab use to format microsatellite data extracted from a custom database system. I have made it available in case it is useful to others. My main objective was to convert from "Raw" format to others. I am motivated by how long I have seen colleagues spend formatting data.

*You can download CONVERT, a program that handles many population genetic formats, and see information on its file format here.

Formats Currently Handled

Infile (Read) Formats	Outfile (Write) Formats
Raw (csv)	Raw (csv)
Genepop	Arlequin(haplotypic)
Convert	Genepop
Arlequin(genotypic)	Immanc/Bayesass+
	Migrate
	NewHybrids
	MSVar
	BAPS
	Structure
	TM3 /CoNe
	TMVP
	MLNE
	MRatio

Installation and Usage

Installation: Formatomatic works on any machine that has a JRE (Java Runtime Environment) installed. It works with Sun's JRE version 1.4.X and 1.6.0. It should easily run on a Windows, MacOS or Linux machines once the JRE is in place. Note that Mac OS X has a JRE already installed. You can run it by double clicking on the jar file or from a command line (see the README file in the archive.)

Usage: Specify an infile name (using the file browser or by typing the full path in directly) and format. Repeat for the outfile. Hit the "convert" button and make certain you carefully check the output. As a rule, all output files will have to be "tweaked" before you analysis program can read them correctly.

Please see the various text files included in the distribution for more details.

Citing Formatomatic

A paper describing Formatomatic has been published in Molecular Ecology Notes. Please cite the program as follows:

Manoukis, N.C. 2007. FORMATOMATIC: A program for converting diploid allelic data between common formats for population genetic analysis. Molecular Ecology Notes, In Press.

Obtaining Formatomatic

Current Stable Version and Past Versions

The program, source code, documentation and sample files are available in the gzipped tar archives below.

Date	Ver	Download	Notes	Comments
May 14 2008	0.8.1	tar.gz (82K)	notes	Bug fixes, no new features
Aug 8 2007	0.8	tar.gz (78K)		1 more read format and 2 write formats, command line mode
Apr 12 2007	0.7	tar.gz (65K)		Better missing data handling, fancier face
Mar 16 2007	0.6.1	tar.gz (46K)		2 more out formats, versioning changes, fixed MSVAR bug
Feb 21 2007	0.5	tar.gz (42K)		2 more out formats, commenting changes, some quotation stripping
Sep 13 2006	0.4	tar.gz (50K)		2 more formats, GUI changes, overwrite warning
Mar 13 2006	0.3	tar.gz (42K)		More formats, better internals
Jul 28 2004	0.2	tar.gz (40K)		Initial Release

Installation and Usage

Installation: Formatomatic works on any machine that has a JRE (Java Runtime Environment) installed. It works with Sun's JRE version 1.4.X in a basic mode or with 1.6.0 for all features. It should easily run on a Windows, MacOS or Linux machines once the JRE is in place. Note that Mac OS X has a JRE already installed, but it is currently an outdated version by default as of this writing (see below for more details). You can run it by double clicking on the jar file or from a command line (see the README file in the archive.)

Usage (in GUI mode): Specify an infile name (using the file browser or by typing the full path in directly) and format. Repeat for the outfile. Hit the "convert" button and make certain you carefully check the output. As a rule, all output files will have to be "tweaked" before you analysis program can read them correctly. There is also a command line method for using Formatomatic (new in version 0.8).

Please see the various text files included in the distribution for more details.

Citing Formatomatic

Comments, Questions and Feature requests

Any are welcome. You can email me at manoukis [a t] unitsci.dyndns.org (replace the [at] with @ and remove spaces.)

Other Conversion Options

Several other programs are available for converting population genetic data between formats used by various analysis programs. Besides the above-mentioned CONVERT by J. Glaubitz, you might take a look at CREATE by J.A. Coombs et al. Both of these handle microsatellite data only, like Formatomatic, and are MS Windows-only. A new and promising effort by H. Lischer, PGDSpider is also available. PGDSpider is multi-platform and works with a new XML-based file format (PGD), enabling it to handle multiple types of genetic data (DNA, RNA, Microsat, SNP, RFLP, AFLP, Frequecy); you can read more about PGD here.

Here's to hoping you never have to format a dataset entirely by hand again.

License

This software is provided under the GPL General Public License. The text is included in the archive.