AstrobioMike GToTree issues

AstrobioMike / GToTree

A user-friendly workflow for phylogenomics

GNU General Public License v3.0

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issues

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hmmsearch issue with large target sequence

#50 gavinmdouglas closed 2 years ago
5
Adding KO scan capabilities and many other improvements

#49 AstrobioMike closed 2 years ago
0
new muscle support

#48 jianshu93 closed 2 years ago
5
Alignment not loaded error during Aligning, trimming, and inserting gap-sequences step

#47 MiAiM closed 2 years ago
4
Failed to make temporary directory

#46 susheelbhanu closed 1 year ago
10
An option to prevent database version check

#45 felixeye closed 2 years ago
5
fasta file has duplicate entries

#44 ReneKat closed 2 years ago
2
GToTree fails to download accessions after updating

#43 lordlouckster closed 2 years ago
2
Some genomes return Est. %% comp: 0.00

#42 lordlouckster closed 3 years ago
4
Add a way to automatically overwrite the directory if current directory already present

#41 lordlouckster closed 3 years ago
1
GToTree not working with files with Windows EOLs

#40 lordlouckster closed 3 years ago
5
No alignments to any genomes

#39 SilasV123 closed 3 years ago
4
THe newest conda installed version offer -H Archaea wrong

#38 jianshu93 closed 3 years ago
5
[Feedback] gtt-gen-SCG-HMMs vs SCG sets wiki instruction output

#37 naturepoker closed 2 months ago
2
Can't' find unzip_rename_cat_genes.sh mentioned in the SCG set instruction page

#36 naturepoker closed 3 years ago
2
bacterial marker set

#35 sarah872 closed 3 years ago
4
[Question] Is there a way to use this with a collection of protein fasta files?

#34 jolespin closed 3 years ago
2
FastTreeMP for multithreading

#33 hyphaltip closed 3 years ago
3
Error:Is the internet connection weak?

#32 agavriilidou closed 3 years ago
1
Should i use the other Pfam_accession?

#31 won9181 closed 3 years ago
7
Universal HMM profile - missing L15 gene?

#30 aiurco closed 3 years ago
4
Process and alignment completed successfully, but .tre file empty

#29 smdabdoub closed 3 years ago
5
SSL certificate of the Pfam webpage has expired

#28 TlaskalV closed 4 years ago
2
Fasta files specified cannot be found

#27 MicroPat007 closed 3 years ago
5
No module named 'Bio' using conda install

#26 fconstancias closed 4 years ago
3
GTDB Downloads

#25 zpimentel closed 4 years ago
3
Expand HMM searching beyond Pfam?

#24 halexand closed 7 months ago
12
Grep for tabs is actually grep for "t"

#23 MrOlm closed 4 years ago
3
Add GTDB functionality

#22 AstrobioMike closed 4 years ago
1
Use labels for accession numbers

#21 sarah872 closed 4 years ago
6
muscle - segmentation fault

#20 sarah872 closed 4 years ago
3
issues running gtotree on cluster

#19 adamsorbie closed 4 years ago
2
Proteins with multiple domains

#18 adityabandla closed 4 years ago
5
Can I build my own HMM file of Single Copy Genes for Eukaryotes using cDNA?

#17 ardy20 closed 4 years ago
1
Whether the software has the ability to run offline？

#16 panxiaoguang closed 4 years ago
3
Added duplicate labels check to file_to_genome_id_map file

#15 vinisalazar closed 4 years ago
2
-m mapping file does not work with full path

#14 vinisalazar closed 4 years ago
11
../gtt-fasta-serial.sh: line 144: esl-sfetch: command not found

#13 Irrussional closed 4 years ago
4
Any ideas for automated generation of a taxon name mapping file?

#12 Anto007 closed 5 years ago
9
conda install errors

#11 hyphaltip closed 4 years ago
1
Handling fragmented/partial genes

#10 adityabandla closed 4 years ago
3
gtt-align-and-trim-parallel killed + alignment not loaded error

#9 naturepoker closed 4 years ago
4
installation instructions with only software dependencies in conda env

#8 taylorreiter closed 5 years ago
2
Install errors with fish shell.

#7 vinisalazar closed 5 years ago
1
Keeping more than the best hit

#6 sergiophyceae closed 2 years ago
2
Error message "-G needs to be between 0-1" whatever value I specify

#5 slambrechts closed 5 years ago
2
Add functionality for accepting amino acid files of gene calls as an input source

#4 AstrobioMike closed 5 years ago
1
Creating HMM profiles

#3 tenguzame closed 4 years ago
11
Pipeline does not fail when bad input files are provided

#2 jmtsuji closed 5 years ago
7
Any way to know the final number of SCGs used in the concatenated alignment

#1 Anto007 closed 5 years ago
7

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