Tag: MAKER

MAKER v3.01.03 – Genome Annotation pipeline

MAKER v3.01.03

:: DESCRIPTION

MAKER is a portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on seusequent runs. MAKER’s inputs are minimal and its ouputs can be directly loaded into a GMOD database.

::DEVELOPER

Yandell Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  MAKER

:: MORE INFORMATION

Citation:

Genome Res. 2008 Jan;18(1):188-96. Epub 2007 Nov 19.
MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes.
Cantarel BL, Korf I, Robb SM, Parra G, Ross E, Moore B, Holt C, Sánchez Alvarado A, Yandell M.

SuGeT – SuperGeneTree maker

SuGeT

:: DESCRIPTION

Given a set of gene trees and a species tree, SuGeT finds a supergenetree of the input trees that minimizes the reconciliation cost with the species tree. A supergenetree is a tree that “contains” all the input gene trees. The user can also specify to preserve the orthology/paralogy relations from the input trees.

::DEVELOPER

MANUEL LAFOND

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SuGeT

:: MORE INFORMATION

Citation

Lafond M, Chauve C, El-Mabrouk N, Ouangraoua A.
Gene Tree Construction and Correction Using SuperTree and Reconciliation.
IEEE/ACM Trans Comput Biol Bioinform. 2018 Sep-Oct;15(5):1560-1570. doi: 10.1109/TCBB.2017.2720581. Epub 2017 Jun 27. PMID: 28678712.

OMIGA 1.0 – Optimized Maker-based Insect Genome Annotation

OMIGA 1.0

:: DESCRIPTION

OMIGA is a pipeline for predicting protein-coding genes from insect genomes

::DEVELOPER

Li Lab: Insect Genomic and Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • mysql(version 5.1 or later versions)
    – abyss(version 1.3.5 or later versions)
    – cegma(version 2.4.0 or later versions)
    – RepeatModeler(version 1.0.5 or later versions)
    – RepeatMasker(version 3.3.0 or later versions）
    – tophat(version 2.0.6 or later versions）
    – Cufflinks(version 2.0.2 or later versions)
    – Augustus(version 2.6.1 or later versions)
    – SNAP(version 2006-07-28 or later versions)
    – GeneMark-es(version 2.3 or later versions)
    – Maker(version 2.26 or later versions）
    – Interproscan(version 4.8 or later versions)

:: DOWNLOAD

 OMIGA

:: MORE INFORMATION

Citation

Mol Genet Genomics. 2014 Aug;289(4):567-73. doi: 10.1007/s00438-014-0831-7. Epub 2014 Mar 9.
OMIGA: Optimized Maker-Based Insect Genome Annotation.
Liu J1, Xiao H, Huang S, Li F.

P-SAMS – the Plant Small RNA Maker Suite

P-SAMS

:: DESCRIPTION

P-SAMS is a web tool for the simple and automated design of artificial miRNAs (amiRNAs) and synthetic trans-acting small interfering RNAs (syn-tasiRNAs) for efficient and specific targeted gene silencing in plants.

::DEVELOPER

the Carrington Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Perl
  • C++ Compiler

:: DOWNLOAD

 P-SAMS

:: MORE INFORMATION

Citation:

P-SAMS: a web suite for plant artificial microRNA and synthetic trans-acting small interfering RNA design.
Fahlgren N, Hill ST, Carrington JC, Carbonell A.
Bioinformatics. 2015 Sep 17. pii: btv534