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Old CEGMA versions

CEGMA v2.4

Download the latest version: cegma_v2.4.010312.tar.gz. Note that older versions of CEGMA are still available. Fixes in the new version include:

• Fixed use of -threads option
• Fixed bug which happened when genome contained no CEGs at all
• Fixed error that could occur when processing some unusual genewise predictions
• Fixed bug in calculating completeness statistics for the subset of 248 highly conserved CEGs
• Made some error messages a little more meaningful

CEGMA v2.3

Latest full distribution: source code and documentation - [DOWNLOAD]

New features included:

• Supports NCBI BLAST+ only (support for WU-BLAST has been removed)
• New --threads option to let you utliize multiple cores when running tblastn and hmmsearch
• Now works with latest versions of HMMER and geneid
• Misc. small improvements to code

CEGMA v2.1

Latest full distribution: source code and documentation - [DOWNLOAD]

New features include:

• New parameters to allow the users to run their favourites protein sets instead of the provided set of KOGS. These variables can be used to run other than default HMM profiles:
  • --prot_num - Number of proteins per family/profile. They have to be in consecutive order in the fasta file (default: 6)
  • --cutoff_file - File with the cutoff for the HMMER alignments (default: $CEGMA/data/profiles_cutoff.tbl)
  • --hmm_prefix - Each protein ID must have "___" followed by the hmmprefix and a number (ex. At3g02190___KOG1762) (default: KOG)
  • --hmm_directory - Directory that contains the hmm files. The files must be named hmm_prefix(number).hmm ex. KOG1762.hmm (default: $CEGMA/data/hmm_profiles)
• New genewise parsing that increases sensitivity.
• Bug fixed. (In short contig sequences (less than 5Kb) predictions in the negative strand had wrong genomic coordinates; now it is fixed !!).

CEGMA v2.0

Full distribution: source code and documentation - [DOWNLOAD]

New features include:

• Genome sequence completeness estimation based on the amount of genes found (see Genome completeness ).
• New parameter --intron_max allows to set a maximum intron length.
• Output file including genomic coordinates.
• Compatible with new release of geneid (v 3.1.7) WARNING !! Last geneid version seems to be not very stable. We strongly recommend geneid v1.2 to be used with CEGMA.

CEGMA v1.0

Full distribution: source code and documentation - [DOWNLOAD]

Content © Korf Lab 2014