GeneOrder statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

GeneOrder specifications

Information


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

Documentation


Maintainer


This tool is not available anymore.

Publications for GeneOrder

GeneOrder citations

 (11)
library_books

Phylogeny analysis from gene order data with massive duplications

2017
BMC Genomics
PMCID: 5657036
DOI: 10.1186/s12864-017-4129-0

[…] Our software package is publicly accessible at http://www.geneorder.org. […]

library_books

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

2017
Hereditas
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 (http://www.geneorder.org/server.php) using the phylogeny obtained in the previous step (outgroup reduced to Biomphalaria) as a fixed tree (ie. Small Parsimony Problem, using SPP option). […]

call_split

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

2017
PeerJ
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 (http://www.geneorder.org/server.php) (). BLASTX homology searches were used to characterize introns and open reading frames (orfs) ≥300 bp with an E-value threshold <1e − 06 (https://blast.ncbi.nlm.nih.gov/blast […]

library_books

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

2016
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). […]

library_books

Comparative analysis of multiple inducible phages from Mannheimia haemolytica

2015
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 […]

library_books

Genome Rearrangements Can Make and Break Small RNA Genes

2015
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. […]

Citations

Looking to check out a full list of citations?

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

GeneOrder reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review GeneOrder