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How to get .anchors file without same query gene in one block just like .collinearity file from old version MCScanX

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When I use `MCscan (Python version)` to get `.anchors` file, some blocks contained Pairwise synteny with same query gene but different subject gene inside the block, which could actually form...

When I'm running `iqtree -s A.trimal -m MFP -bb 1000 -bnni -pre A -st AA -redo -T AUTO`, I got the error information as blow: WARNING: Please only use GTR20...

filterBAM_forHiC.pl error

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Hi Dr.zhang Thanks your great work in ALLHIC ! I got an error when I run `filterBAM_forHiC.pl sample.bwa_aln.REduced.paired_only.bam sample.clean.sam`. There is no header information in `sample.clean.sam`, which casued error ([main_samview]...

update syngap to v1.2.0

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Describe your pull request here ---- Please read the [guidelines for Bioconda recipes](https://bioconda.github.io/contributor/guidelines.html) before opening a pull request (PR). ### General instructions * If this PR adds or updates a...

Describe your pull request here ---- Please read the [guidelines for Bioconda recipes](https://bioconda.github.io/contributor/guidelines.html) before opening a pull request (PR). ### General instructions * If this PR adds or updates a...

trouble in Azure DevOps test

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I have been experiencing this error continuously during the automatic testing process since submitting the update, but I have not been able to find the cause. It seems that there...

several issues in the ruuning of EDTA2

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Hello, thanks for your development of this useful tools! I met several issues when use EDTA2: 1) the file `$genome.EDTA.TEanno.split.density` didin't show the running result but the following content ...

error with mummerCoordsDotPlotly.R

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Hello I met the following error message when use mummerCoordsDotPlotly.R. What's the reason for this error? 

Hello~ Thanks for developing such powerful tools. I met the issue when I run `mash sketch -m 2 01.ccs.fq.gz -k 27 -p 5`, and the warning message is `WARNING: The...