Homework practices that are missing programs or have other issues.
Please edit this page to describe any broken links, uninstalled software or other issues that you find with the lab pages.
URL: http://biowiki.org/view/Teaching/PrimatePhylogeny
Date reported: Mon, Nov 10 2008
Reported by: Gabriel Lopez
Description: Missing distance matrix software
At this part:
- If a site "has not experienced a mutation", is this the same as saying that "the human and chimp amino acids are identical"? If not, why not -- and how would this affect your analysis?
- Estimate a "distance matrix" for these species:
~be131/dart/bin/tkfdistance --nocountindel -log 6 ATP6.stockholm >ATP6.distance
- What do the entries of the distance matrix represent?
- (See if you can answer this by e.g. searching for "phylogenetic distance matrix" on Google; if not, ask your neighbor, the professor or the GSI.)
- Estimate a tree by "weighted neighbor-joining"
~be131/dart/bin/weighbor -i ATP6.distance -o ATP6.tree -vvv
Fixed by IanHolmes, 5:24pm 11/10, by updating & rebuilding DART, as follows: cd ~be131/dart; cvs up; make
URL: http://biowiki.org/twiki/pub/Teaching/InformationContentHomework/tRNA.stock
Date reported: Mon, Nov 10 2008
Reported by: Sonny Hernandez
Description: Broken link needed for HW write-up.
Link fixed by IanHolmes to point back to InformationContentOfDNA page, 6:35pm 11/10 | 
