SynMap statistics

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Citations per year

Number of citations per year for the bioinformatics software tool SynMap
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Tool usage distribution map

This map represents all the scientific publications referring to SynMap per scientific context
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Associated diseases

This word cloud represents SynMap usage per disease context
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Popular tool citations

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Protocols

SynMap specifications

Information


Unique identifier OMICS_13395
Name SynMap
Interface Web user interface
Restrictions to use None
Input data Putative genes or regions of homology between two genomes
Output data Log file, homolog search, diagonals and results.
Programming languages Python
License MIT License
Computer skills Basic
Stability Stable
Maintained Yes

Subtool


  • FractBias

Documentation


Maintainer


  • person_outline Eric Lyons

Additional information


https://genomevolution.org/wiki/index.php/FractBias

Information


Unique identifier OMICS_13395
Name SynMap
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Putative genes or regions of homology between two genomes
Output data The graphical output of FractBias is composed of subplots for each target genome chromosome.
Operating system Unix/Linux
Programming languages Python
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes

Subtool


  • FractBias

Download


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Versioning


No version available

Documentation


Maintainer


  • person_outline Eric Lyons

Additional information


https://genomevolution.org/wiki/index.php/FractBias

Publications for SynMap

SynMap citations

 (80)
library_books

Resolution effects in reconstructing ancestral genomes

2018
BMC Genomics
PMCID: 5954274
PMID: 29764371
DOI: 10.1186/s12864-018-4462-y

[…] lants, the processes of whole genome duplication and fractionation compound inherent inferential difficulties due to genome rearrangement. A telling aspect in the widely-used synteny block identifier SYNMAP [, ] is the default requirement that at least five pairs of orthologous genes in two genomes or five pairs of paralogous genes in a single genome, in close succession, are necessary before we h […]

library_books

A tutorial of diverse genome analysis tools found in the CoGe web platform using Plasmodium spp. as a model

2018
PMCID: 5887277
DOI: 10.1093/database/bay030

[…] Find SynMap on CoGe’s main page (https://genomevolution.org/CoGe/SynMap.pl).Search for and select the desired genome for Organisms 1 and 2 [e.g. type Plasmodium in the ‘Search’ box for Organism 1 and selec […]

library_books

Patterns of Population Variation in Two Paleopolyploid Eudicot Lineages Suggest That Dosage Based Selection on Homeologs Is Long Lived

2018
Genome Biol Evol
PMCID: 5887293
PMID: 29617811
DOI: 10.1093/gbe/evy061

[…] We obtained pairs of At-α duplicates using CoGe’s SynMap algorithm () and merged this list with the At-α duplicates reported by using version 10.02 of the Arabidopsis thaliana Col-0 genome as our reference (). We excluded from our ohnolog lists any […]

library_books

Improved Genome Assembly and Annotation for the Rock Pigeon (Columba livia)

2018
PMCID: 5940132
PMID: 29519939
DOI: 10.1534/g3.117.300443

[…] lies were hard masked using NCBI WindowMasker () and genome-wide alignments were calculated with LAST (). From these alignments, a genome-scale dotplot indicating syntenic regions was generated using SynMap (; ).The colLiv2 assembly is currently unannotated. Therefore, to compare gene content between assemblies, we estimated the number of annotated Cliv_2.1 genes absent from colLiv2 based on gene […]

call_split

Chromosome scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data

2018
PMCID: 5802725
PMID: 29423238
DOI: 10.1038/s41438-017-0013-y
call_split See protocol

[…] Syntenic dot plots were generated with SynMap using LAST for whole-genome comparisons. A minimum of five synteny genes with a maximum distance of 50 kb between adjacent genes was used to seed a syntenic block. Syntenic gene pairs were colo […]

library_books

Phylogenomics of the olive tree (Olea europaea) reveals the relative contribution of ancient allo and autopolyploidization events

2018
BMC Biol
PMCID: 5785856
PMID: 29370802
DOI: 10.1186/s12915-018-0482-y

[…] ed olive and oleaster and, hence, must have predated the domestication of the species. This is confirmed when using the number of synonymous substitutions per synonymous site (KS) values predicted by Synmap when comparing the two O. europaea genomes. The KS graph provided by Synmap presents five peaks (See Additional file : Figure S11c). The first is formed by proteins that were identical between […]


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SynMap institution(s)
BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA; Genetis GIDP, University of Arizona, Tucson, AZ, USA; Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
SynMap funding source(s)
This work has been supported by the U.S. National Science Foundation (IOS – 1339156 and IOS – 1444490).

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