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GeneOrder specifications


Unique identifier OMICS_17813
Name GeneOrder
Interface Web user interface
Restrictions to use None
Programming languages Java, Perl
Computer skills Basic
Version 2.0
Stability No
Maintained No



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Publications for GeneOrder

GeneOrder citations


Phylogeny analysis from gene order data with massive duplications

BMC Genomics
PMCID: 5657036
DOI: 10.1186/s12864-017-4129-0

[…] Our software package is publicly accessible at […]


The complete mitogenome of Orcula dolium (Draparnaud, 1801); ultra deep sequencing from a single long range PCR using the Ion Torrent PGM

PMCID: 5379511
PMID: 28396619
DOI: 10.1186/s41065-017-0028-2

[…] An ancestral gene order reconstruction [] was done using the Maximum Likelihood Gene Order analysis (MLGO) web server ( using the phylogeny obtained in the previous step (outgroup reduced to Biomphalaria) as a fixed tree (ie. Small Parsimony Problem, using SPP option). […]


Plastomes of the green algae Hydrodictyon reticulatum and Pediastrum duplex (Sphaeropleales, Chlorophyceae)

PMCID: 5437862
PMID: 28533973
DOI: 10.7717/peerj.3325
call_split See protocol

[…] d synteny maps were generated using the Mauve plugin () with default settings in Geneious. Gene order analyses were performed using MLGO: Maximum Likelihood Gene Order Analysis web server ( (). BLASTX homology searches were used to characterize introns and open reading frames (orfs) ≥300 bp with an E-value threshold <1e − 06 ( […]


Comparative analyses of chloroplast genome data representing nine green algae in Sphaeropleales (Chlorophyceae, Chlorophyta)

PMCID: 4802548
PMID: 27054159
DOI: 10.1016/j.dib.2016.03.014

[…] were performed for two sets of species (, ). Gene order data were scored for 15 taxa in the class Chlorophyceae (GeneOrder.txt). A phylogenetic analysis of gene order using Badger is presented in (, GeneOrder.tre). […]


Comparative analysis of multiple inducible phages from Mannheimia haemolytica

BMC Microbiol
PMCID: 4553209
PMID: 26318735
DOI: 10.1186/s12866-015-0494-5

[…] reference genome of 3927AP1 the majority of dissimilar regions were observed in 27.6-29.7 Kb of 535AP2, 24.8-48.2 Kb of 587AP2 and 1.7-15.2 Kb regions of 1152AP2 (Fig. ). Likewise, comparative using GeneOrder4.0 [] showed that 3927AP1 and 1152AP2 shared 72 (91.1 %) and 52 (65.8 %) of homologs with 535AP2. Phage 1152AP2 shares 62 (74.7 %) homologs in common with 3927AP1. Again, 587AP2 is very dist […]


Genome Rearrangements Can Make and Break Small RNA Genes

Genome Biol Evol
PMCID: 4350180
PMID: 25601101
DOI: 10.1093/gbe/evv009

[…] Orthologous genes common to E. coli and Salmonella were identified using a reciprocal BLAST best-hit approach (). Gene order of each orthologous gene-pair was determined with GeneOrder 4.0 (), and in cases where the genomic locations were not syntenic in the two species, we searched for gene-pairs with adjacent novel IGRs using Artemis. […]


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GeneOrder institution(s)
School of Computational Sciences, George Mason University, Manassas, VA, USA; Bioinformatics Program, American Type Culture Collection, Manassas, VA, USA

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