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Hi，
I'm new to this and I want to construct a recombination free core SNP phylogenetic tree using snippy and gubbins.
I'm confused because core.aln is a core SNP alignment file and core.full.aln is…
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Hi,
I have been using minimap2 for many genome to genome alignments and I have noticed an odd pattern.
If I take a large genome like a human genome and align (paf output) the whole chromosomes …
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Hi,
I am classifying Phages according to their taxonomy. I am having the issue that my fast afiles have fractions of the genome instead of the whole genome:
My fasta files have the format
Geno…
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Hello,
I am trying to run homoplasyFinder (R) on set of whole genome multi-fasta alignment. The file have gaps. I run to the following error. If feedback on the wright way would be helpful.
```
…
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Hi,
We have been using SyRI for two-genome comparison in multiple species pairs, and issue #48 has been helpful in fixing problems whenever "Index out of range" error shows up. The chromosomes to re…
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Hi Paul,
Amazing software!
I have several questions about the HyDe. I see the input data should be diploid data or ambiguous sites. But here I have a diploid species and tetraploid species, an…
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Dear Authors,
thank you very much for providing the pipeline! I would like to run the pipeline on different genomes together to compute whole genome alignment of different species to use them afte…
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-searching for reference exome (CDS) as a reference for our exome sequence data due to several reasons:
1- when we aligned to one chromosome like chr 20, the alignment rate was v.v low 2.8%
2- whe…
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Hello,
I seem to miss something in the algorithm, could you please specify how do you reject a read from being mapped without identity threshold? Or there is one implicitly?
Thank you!
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Hi
In the Cactus paper (https://www.biorxiv.org/content/10.1101/730531v3) it mentions that it expects the input genomes to be soft-masked. I was wondering how Cactus treats the soft-masked regions.…