Difference between revisions of "Cypridinidae Phylogeny"
From Ucsbgalaxy
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==Data Sources== | ==Data Sources== | ||
| + | ===Compiled=== | ||
| + | * THO is compiling all raw datasets on the Osiris demo server [[ http://galaxy-dev.cnsi.ucsb.edu/osiris/u/ostratodd/h/cypridinidae-raw-data-sets]] | ||
===Morphological matrix=== | ===Morphological matrix=== | ||
* Cohen and Morin (2003) | * Cohen and Morin (2003) | ||
Revision as of 12:30, 25 September 2013
Contents
Data Sources
Compiled
- THO is compiling all raw datasets on the Osiris demo server http://galaxy-dev.cnsi.ucsb.edu/osiris/u/ostratodd/h/cypridinidae-raw-data-sets
Morphological matrix
- Cohen and Morin (2003)
- Uploaded to MorphoBank
- Requires conversion of species names to match other data
- Partly done, but needed for some data partitions
Lisa Torres Matrix
- Thesis of Vanessa Gonzalez
- 16S, COI, 12S and H3 genes
Transcriptome Data
- Oakley et al (2013) included Skogsbergia lerneri and Vargula tsujii [[1]]
- OET13 included Regier (2010) data in S. lerneri
- von Reumont (2011) included 1 undescribed species. Based on collection locality in Mediterranean, this is likely Skogsbergia [[2]]
- We have multiple new transcriptomes that we used for finding luciferases
GenBank Data
- 18S
- 16S
- Wakayama see table 1 [[5]]
TO DO
- In MorphoBank, Create separate partitions for binary and multi
- Full mt genomes could be useful and might be present in transcriptomes. Make HMM set for ostracod mt genomes using V. hilgendorfii and Argulus(?)
