Agora

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drawKaryotype trouble

1

Hello, Firstly, thank you for such great software as AGORA. I am really sorry to disturb you, but I have met issues in reconstructed blocks visualization with misc.compareGenomes in recent...

Alchimic007

Orthology groups correspond to HOGs?

2

Hello, Thanks for developing such useful tools. I want to use AGORA with providing the orthologous groups files and not the trees; I have a question regarding these orthology groups....

alexvasilikop

``` ------------------------------------------------------------------------------------------------------------------------------ | Key | Values | ------------------------------------------------------------------------------------------------------------------------------ | speciesTree | ~/agora/Agora_data/SpeciesTree_rooted_node_labels.txt | | orthologyGroups | ~/agora/Agora_data/orthoGroups/orthologyGroups.%s.list | | IN.genesFiles | ~/agora/Agora_data/genelists/genes.%s.list | | OUT.ancGenesFiles | ancGenes/all/ancGenes.%s.list.bz2 | | OUT.genesFiles...

hyBio

Dear Agora Team, I extend my gratitude to you for developing this exceptional tool for reconstructing ancestral genomes. Recently, I've encountered some challenges in accurately identifying breakpoints between successive genomes...

Caoyu819

Creating input for analysis

4

Hi Agora-team, I have been trying to learn how to construct ancestral genome karyotype for ever, and was never been able to understand it properly and then saw your paper...

amit4mchiba

Dear AGORA team, I'm currently working on genome structure evolution in the Fagales order. Your AGORA pipeline has been incredibly helpful, aiding me in reconstructing ancestral genomes. Thanks for this...

Caoyu819

delehef

Can Nexus format tree replace NHX format tree?

2

Thanks a lot for convenient tools. I have question about input gene tree. Can Nexus format tree replace NHX format tree? Or you have recommend methods transfrom Nexus format tree...

zhangzhiyangcs

Visualization of results

1

Hi Ahora team, I wonder if you have an advice on how to visualize Ahora results. There are really nice plot on you last paper that seems similar to the...

DiegoSafian

how to deal with many CARs

4

Dear Agora group, I am reconstructing ancestral gene orders using the AGORA software. The main challenge I am facing is that I have identified hundreds of CARs with decreasing numbers...

shuiyanwu778