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(Copied from the lastz mailing list)
we have run lastz version 1.04.15 with --queryhsplimit=keep,nowarn:200 on two softmasked mammalian genomes. The masking comes from repeatMasker. The reason for …
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Is there a way to increase the visibility of SNPs at wider views? In the example below, I can see SNP differences between alignments in a 56 kb window, but not in a 140 kb window, which encompasses th…
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jcvi.graphics.ribbon module is a modified version of the synteny module which allows plotting of arbitrary alignments and multiple genomic feature tracks. Ribbon plots are not based on ortholog linkag…
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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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Hi,
I used MAFFT for multiple alignments of the whole genome. However, it generates a fasta format. When I use this fast format alignment file, RAxML uses only one thread instead of multiple threads…
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Hi,
Thanks for developing phastSim - a lovely tool.
I just have a quick question regarding how phastSim adjusts genomic positions when insertions and deletions are added to the genomes: when sub…
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Hi, glennhickey,
I'm sorry to bother you, but I have a problem that has been troubling me for a long time and I need your help.
I have a whole-genome alignment result for 300 species using cactu…
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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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This error appears to be similar to #1466
After running for a few weeks on ~50 mammalian fastas from NCBI, cactus crashes with two seemingly related errors from a bunch of toil jobs. I'm wondering…
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Curate test data sets on AWS, preferably on S3 open data, this may include, germline, tumor/normal, genotype, RNASeq data.