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Hi all and thanks for your work. According to the documentation, "The first step in any Tombo analysis is to re-squiggle (raw signal to reference sequence alignment) raw nanopore reads. This creates a…
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Is it possible to write alignments to file?
E.g. I want to process an existing .bam file by removing a part of the sequence. How do I do that?
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Hello,
I am currently working with whole-genome alignments generated using Cactus. I used phastCons to predict conserved elements and then employed phyloP to detect lineage-specific accelerated ele…
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Keep reference sequence fixed at the top (like currently in pairwise alignments) when scrolling through the alignment view after aligning seq reads to a ref seq
![Screen Shot 2018-07-06 at 7.12.03 PM…
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Download and prepare ColabFoldDB on the cluster.
> ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures. They ar…
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Hi there!
FIrst off, thanks for your great work on this.
I've been having heaps of fun trying to figure out working combinations of different genome graph tools over the last few weeks.
I'm run…
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I am building a custom database according the instructions in the user guide. I would like to understand more specifically how cstranslate converts an alignment to an abstract state alphabet. In parti…
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1. Create one container with all dependencies
Pipeline:
1. cmalign query sequences to 16s profile
2. esl-alimerge query and reference alignments
3. pplacer
4. guppy classifications classificati…
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Hello,
In the paper about A. laboriosa, you estimated divergence time among species based on the concatenated alignments of 4-fold degenerate sites from single-copy genes using MCMCtree in PAML v4.…
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I am using the sequence to be run on http://opig.stats.ox.ac.uk/webapps/newsabdab/sabpred/anarci/ QVQLVESGGGVVQPGRSLRLSCAASGFTFSVYGMNWVRQAPGKGLEWVAIIWYDGDNQYYADSVKGRFTISRDNSKNTLYLQMNGLRAEDTAVYYCARDLRT…