mptrsen Orthograph issues

mptrsen / Orthograph

Orthology prediction using a graph-based, reciprocal approach with profile hidden Markov models

GNU General Public License v3.0

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issues

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Which gz file in OB11 should I download?

#40 auto-simi opened 3 months ago
0
Under utilization of computational resources in cluster

#39 CristianBezaBeza opened 1 year ago
1
--cog-list-file

#38 CristianBezaBeza opened 2 years ago
3
Identical gene names in different official gene sets lead to an omission of these genes

#37 cmayer opened 3 years ago
0
How to launch multiple Orthograph instances using the same database?

#36 linzhi2013 closed 4 years ago
1
bug? Orthograph cannot use anymore the PARALLEL::ForkManager

#35 kmeusemann closed 4 years ago
4
Slow orthograph-analyzer

#34 KristinaGagalova closed 4 years ago
2
Option to only map a single contig to ortholog

#33 JMPflug closed 5 years ago
3
Inputting amino acid sequences

#32 austinv11 closed 4 years ago
3
Resuming orthograph runs?

#31 jsoghigian closed 4 years ago
2
Can't locate object method "new"

#30 Arctictern6 closed 6 years ago
3
Orthograph loads 0 COGs from a custom orthogroup description file

#29 claumer closed 6 years ago
2
Deal with empty lines in input tables

#28 mptrsen closed 4 years ago
0
ForkManager eludes the test

#27 nylander closed 4 years ago
1
Permission/path for swipe?

#26 zjlahey closed 7 years ago
1
Issue with swipe.pm

#25 zjlahey closed 7 years ago
1
Old Mac linebreaks

#24 mptrsen closed 4 years ago
1
--help without --configfile

#23 alephreish opened 8 years ago
0
RealBin

#22 alephreish closed 7 years ago
2
Automate COG table import

#21 mptrsen opened 8 years ago
1
Selenocysteine (U) is not replaced with X in OGS sequences

#20 mptrsen closed 4 years ago
0
Concatenated sequences sometimes have more X's than necessary

#19 mptrsen closed 4 years ago
0
Extend ORF beyond the HMM alignment region

#18 mptrsen closed 9 years ago
0
Catch SIGINTs during exhausting the database in reporter

#17 mptrsen closed 4 years ago
0
Improve robustness in the case of network downtime

#16 mptrsen closed 10 years ago
0
Concatenation is made optional

#15 mptrsen closed 10 years ago
1
Write a sequence class.

#14 mptrsen opened 11 years ago
0
Check whether the program executables exist where specified.

#13 mptrsen closed 9 years ago
0
Output fasta files

#12 mptrsen closed 10 years ago
1
Output corresponding nucleotide sequences along with the peptide sequences

#11 mptrsen closed 10 years ago
1
Make all config file options available as command line options

#10 mptrsen closed 11 years ago
2
Outsource all MySQL functions into a module

#9 mptrsen closed 10 years ago
1
Add an option to list ortholog set content

#8 mptrsen closed 12 years ago
1
Every time something is added to the ortholog set, rebuild the BLAST database.

#7 mptrsen closed 10 years ago
2
Only fasta files with an OrthoDB-style header are accepted by default.

#6 mptrsen closed 12 years ago
1
BLAST input files are checked for validity during upload

#5 mptrsen closed 12 years ago
1
Use Exonerate to check for correspondence

#4 mptrsen closed 10 years ago
0
Concatenation is made optional

#3 mptrsen closed 11 years ago
1
Transcript domains are used instead of entire transcripts

#2 mptrsen closed 11 years ago
3
Orthology is not established until the end of the analysis

#1 mptrsen closed 11 years ago
2