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EvidentialGene is a genome informatics project for Evidence Directed Gene Construction for Eukaryotes (animals and plants). This is a public discussion + announcement group for EvidentialGene users, including biologists and engineers of genome information. Project software is available at https://sourceforge.net/projects/evidentialgene/ and http://arthropods.eugenes.org/EvidentialGene/ with Evigene sets for several animals and plants at the later site.

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10/24/25

RNA Sequencing Data with R/Bioconductor course

Dear all, join our RNA Sequencing Data with R/Bioconductor course, held online 3–14 November 2025,

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RNA Sequencing Data with R/Bioconductor course

Dear all, join our RNA Sequencing Data with R/Bioconductor course, held online 3–14 November 2025,

10/24/25

Jeferson Alexis Durán Fuentes, Don Gilbert3

10/14/25

High duplication in my transcriptome in BUSCO using tr2aacds4.pl

Hi Don, I understand, I omitted the ct-hit-est step. As part of my methods, I am using Kraken2 and

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High duplication in my transcriptome in BUSCO using tr2aacds4.pl

Hi Don, I understand, I omitted the ct-hit-est step. As part of my methods, I am using Kraken2 and

10/14/25

9/24/25

Physalia online course: Sex Chromosome Evolution (6–10 October)

Dear colleagues, Registration is still open for the Physalia online course: Sex Chromosome Evolution

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Physalia online course: Sex Chromosome Evolution (6–10 October)

Dear colleagues, Registration is still open for the Physalia online course: Sex Chromosome Evolution

9/24/25

5/19/25

Do DNA and cytometric measures agree on genome sizes?

Find a detailed answer to this question in Gnodes#4 draft document Your comments are welcome (note

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Do DNA and cytometric measures agree on genome sizes?

Find a detailed answer to this question in Gnodes#4 draft document Your comments are welcome (note

5/19/25

berger juliette, Don Gilbert4

4/11/25

Issue with transcriptome completeness after applying EvidentialGene

Le jeu. 10 avr. 2025, 15:05, berger juliette <bergerju...@gmail.com> a écrit : Hello Don

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Issue with transcriptome completeness after applying EvidentialGene

Le jeu. 10 avr. 2025, 15:05, berger juliette <bergerju...@gmail.com> a écrit : Hello Don

4/11/25

Laureano Jose Giordano, Don Gilbert2

3/6/25

Question about duplicate ID warning in Evigene

Laureano, I suspect this is an ID format problem, the same trinity ID is being used for two ORFs

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Question about duplicate ID warning in Evigene

Laureano, I suspect this is an ID format problem, the same trinity ID is being used for two ORFs

3/6/25

8/5/24

Gnodes#2: the long and short of it .. early draft doc

Dear readers, Find here an early draft of a long, and still messy, document on measuring genomes with

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Gnodes#2: the long and short of it .. early draft doc

Dear readers, Find here an early draft of a long, and still messy, document on measuring genomes with

8/5/24

4/20/24

Re: Queries related to Evigene for my work

"..We generated RNA-seq (Illumina) and Iso-seq (PacBio) data .. built transcripts with these

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Re: Queries related to Evigene for my work

"..We generated RNA-seq (Illumina) and Iso-seq (PacBio) data .. built transcripts with these

4/20/24

Laureano Jose Giordano, Don Gilbert2

4/20/24

Question about missing genes

Dear Laureano and others, This is a common question, that BUSCO scores of Evigene's, or any

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Question about missing genes

Dear Laureano and others, This is a common question, that BUSCO scores of Evigene's, or any

4/20/24

Yuwei Xiao, Don Gilbert2

4/20/24

Some questions before EvidentialGene usage

Dear Yuwei and other readers, My apologies in the long delay answering this .. I've been stuck

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Some questions before EvidentialGene usage

Dear Yuwei and other readers, My apologies in the long delay answering this .. I've been stuck

4/20/24

June Ordoñez, Don Gilbert2

2/20/24

generate gff/gtf from the okay set

You may want to use the gtf from transdecoder, as I don't know what data this software scRNAseq

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generate gff/gtf from the okay set

You may want to use the gtf from transdecoder, as I don't know what data this software scRNAseq

2/20/24

12/25/23

Holiday 2023 Genomics Puzzle

Solve this puzzle .. and/or read how I did. Your comments are desired. Cytometric methods of genome

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Holiday 2023 Genomics Puzzle

Solve this puzzle .. and/or read how I did. Your comments are desired. Cytometric methods of genome

12/25/23

Karen Daiana Schoninger, Don Gilbert2

12/5/23

#t2ac: FATAL ERR: 30568 duplicate ids in transcripts.aa

You want to use trformat.pl to ensure unique ids for your input transcript set: evigene/scripts/

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#t2ac: FATAL ERR: 30568 duplicate ids in transcripts.aa

You want to use trformat.pl to ensure unique ids for your input transcript set: evigene/scripts/

12/5/23

charles...@gmail.com, Don Gilbert2

11/16/23

Cleaning up the transcriptome results from tr2aacds.pl?

Charles, This updated tr2aacds program has changed the folder name 'publicset' to '

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Cleaning up the transcriptome results from tr2aacds.pl?

Charles, This updated tr2aacds program has changed the folder name 'publicset' to '

11/16/23

10/24/23

Gnodes/Genome Depth Estimator paper #3

Dear genome/gene biologists and informaticians, A Gnodes#3 draft document is here, not quite finished

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Gnodes/Genome Depth Estimator paper #3

Dear genome/gene biologists and informaticians, A Gnodes#3 draft document is here, not quite finished

10/24/23

Iuri Silva, Don Gilbert4

9/22/23

ERR=134 tr2ncrna.pl

Dear Dr. Gilbert, I was able to overcome the previous issue by splitting the input into multiple

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ERR=134 tr2ncrna.pl

Dear Dr. Gilbert, I was able to overcome the previous issue by splitting the input into multiple

9/22/23

Eric Edsinger, Don Gilbert2

7/31/23

Gnodes using only BUSCO genes as cds

Eric, Thanks much for your interest and questions about Gnodes. I'll be happy to help you, and

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Gnodes using only BUSCO genes as cds

Eric, Thanks much for your interest and questions about Gnodes. I'll be happy to help you, and

7/31/23

7/19/23

Re: [evidentialgene] Is it possible to search CDS just in the + strand using tr2aacds.pl?

The current release of EvidentialGene tr2aacds.pl pipeline for RNA assembly now auto-detects stranded

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Re: [evidentialgene] Is it possible to search CDS just in the + strand using tr2aacds.pl?

The current release of EvidentialGene tr2aacds.pl pipeline for RNA assembly now auto-detects stranded

7/19/23

Eric Edsinger, Don Gilbert2

7/17/23

How to identify isoforms post-Evigene

Eric, Something is wrong, but your log file doesn't make it clear what. Your output >

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How to identify isoforms post-Evigene

Eric, Something is wrong, but your log file doesn't make it clear what. Your output >

7/17/23

Salvador Gonzalez Juarez

1/5/23

Is it possible to avoid ORF searching in "-" strand using tr2aacds.pl

Dear Dr. Gilbert, First, let me thank you very much for making EvidentialGene. I am using tr2aacds.pl

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Is it possible to avoid ORF searching in "-" strand using tr2aacds.pl

Dear Dr. Gilbert, First, let me thank you very much for making EvidentialGene. I am using tr2aacds.pl

1/5/23

Harish K, Don Gilbert2

12/31/22

Setting up -pHeterozygosity parameter

Harish, A quick answer from tr2aacds.pl -help -pHeterozygosity=[0..9] : reduce percent identities for

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Setting up -pHeterozygosity parameter

Harish, A quick answer from tr2aacds.pl -help -pHeterozygosity=[0..9] : reduce percent identities for

12/31/22

Aaqib Javid, Don Gilbert4

12/20/22

Error while running traacds4.2aa.pl script

The SRA2Genes pipeline in EvidentialGene includes protein annotation via blast to reference proteins,

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Error while running traacds4.2aa.pl script

The SRA2Genes pipeline in EvidentialGene includes protein annotation via blast to reference proteins,

12/20/22

Sai Reddy Achakkagari, Aaqib Javid3

12/14/22

Error: FATAL Missing mrna

Hey, Thanks! It was resolved after Don suggested me to change the file name, the special characters

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Error: FATAL Missing mrna

Hey, Thanks! It was resolved after Don suggested me to change the file name, the special characters

12/14/22

James Ord, Don Gilbert6

11/14/22

tr2ncrna.pl FAILED at step: make_allevdtab

Hi Don By wrong invocation, do you mean specifying the dropset instead of the full transcript set as

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tr2ncrna.pl FAILED at step: make_allevdtab

Hi Don By wrong invocation, do you mean specifying the dropset instead of the full transcript set as

11/14/22

Holly Williams, Don Gilbert3

10/22/22

Thank you for your thorough reply, Don! I am quite new to coding and completely new to Evigene. As

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Thank you for your thorough reply, Don! I am quite new to coding and completely new to Evigene. As

10/22/22

MF, Don Gilbert2

6/13/22

step 9e - hmmscan with Dfam database

However, this does not generate a script for step 9e. Q1: What would be the proper way to generate

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step 9e - hmmscan with Dfam database

However, this does not generate a script for step 9e. Q1: What would be the proper way to generate

6/13/22

6/13/22

draft at bioRxiv: Genes ruler for genomes, Gnodes, measures assembly accuracy

Dear all, Gnodes public draft paper is available since last month. Anyone who tries this new Evigene

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draft at bioRxiv: Genes ruler for genomes, Gnodes, measures assembly accuracy

Dear all, Gnodes public draft paper is available since last month. Anyone who tries this new Evigene

6/13/22

1/13/22

evigene22jan14 software update for Gnodes

evigene22jan14.tar update is available at http://arthropods.eugenes.org/EvidentialGene/other/

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evigene22jan14 software update for Gnodes

evigene22jan14.tar update is available at http://arthropods.eugenes.org/EvidentialGene/other/

1/13/22

Shankar Chereddy, Don Gilbert3

12/13/21

Error running test data

Dear Dr. Don Gilbert I actually changed the path for all the programs required in the "

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Error running test data

Dear Dr. Don Gilbert I actually changed the path for all the programs required in the "

12/13/21

Joanna R., Don Gilbert3

12/6/21

Local directories and single-end data

Dear Don, Thanks, that's very helpful! And the sample data are definitely helpful - the pipeline

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Local directories and single-end data

Dear Don, Thanks, that's very helpful! And the sample data are definitely helpful - the pipeline

12/6/21

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