# 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