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palfinder specifications


Unique identifier OMICS_00111
Name palfinder
Software type Application/Script
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Roche
Operating system Unix/Linux, Mac OS
Programming languages Perl
License GNU General Public License version 2.0
Computer skills Advanced
Version 0.02.04
Stability Stable
Maintained Yes




No version available

palfinder citations


Development of microsatellite loci of pod mahogany, Afzelia quanzensis (Fabaceae), by Illumina shotgun sequencing, and cross amplification in A. africana1

Appl Plant Sci
PMCID: 4915920
PMID: 27347453
DOI: 10.3732/apps.1600010

[…] encer (Illumina, San Diego, California, USA).The resulting raw Illumina paired-end sequencing reads were analyzed with a Perl script, PAL_FINDER_v0.02.04 (available at, which identifies microsatellite loci without the need for prior sequence trimming and assembly (). The Perl script was run with Primer3 version 2.0.0 () for simultaneous primer design. Def […]


Microsatellite loci discovery from next generation sequencing data and loci characterization in the epizoic barnacle Chelonibia testudinaria (Linnaeus, 1758)

PMCID: 4878368
PMID: 27231653
DOI: 10.7717/peerj.2019
call_split See protocol

[…] ity-checked paired-end reads with FastQC (). The software FastqMcf was used to trim adapters, cut low quality ends and remove low quality reads and their mate-pair read ().We executed the perl script palfinder to identify short sequence repeat regions (). The script also calls Primer3, version 2.0.0, to identify potential primer pairs that span the repeat region (). The minimum number of repeat un […]


Using Next Generation RAD Sequencing to Isolate Multispecies Microsatellites for Pilosocereus (Cactaceae)

PLoS One
PMCID: 4641700
PMID: 26561396
DOI: 10.1371/journal.pone.0142602

[…] A variety of software is available to identify microsatellites in NGS datasets (MISA, palfinder, MSATCOMMANDER, QDD), and all of these can effectively process data from 454 and Illumina platforms. QDD is an open acess program, and among the most user-friendly and versatile of the softw […]

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