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# System prepended metadata

title: Angiosperms353v2

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# Angiosperms353v2

Increasing sequence length for poor recovery regions of the phylogeny

Norm: de novo design using primarily genomes
- more quality filtering of gene length
- then re-do the clustering
- tracking gene ID
- What is the best set of input data?
    - Genomes only allows us to track intron positions
    - Transcriptomes could increase sequence diversity


Bill: do we need to help design taxon-specific groups (Rosales, Monocots)
- Norm: focus on universal kit, make tools that help design new custom kits
- Chris: could modify the BYO transcriptomes script from Probes

Bill: getting in front of criticisms of v1
- PAFTOL could re-enrich existing libraries
- improving especially for non-grass monocots

Matt: Coming up with in silico tests for improvements
- making target files for different groups
- On-target percentages
    - BWA vs Diamond with different ways that count "mapping"
    - Duplicate read issues
    - Mapping afterwards
    - Differences between PAFTOL and Johnson Lab on target % 


Minor points

Alex: do we need Amborella?

Chris: Non-homology of a gene with two paralogs in the PAFTOL data 
