Below you will find links to the results of running matrixgen on several different aligned protein datasets. Many of these alignments were originally obtained from the PFAM database. You will find a link to the pfam entry in every matrixgen results page. If there is no PFAM link the data was not obtained from the PFAM database.
The results pages have interesting information about or generated from each alignment. There will be 3 scoring matrices, 3 distance matrices, observed and expected probability of transitions, as well as information on the overall amino acid composition of the alignment. If you have a protein you would like posted, send the compressed data to me (in Nexus format or a2m format) and I will be happy to post it.
|Cox1||Cytochrome C and Quinol oxidase polypeptide I|
|Globin||Globin Seed Alignment|
|GP120||Envelope glycoprotein GP120|
|GP120||Yamaguchi alignment GP120|
|HVC_NS1||Hepatitis C virus non-structural protein E2/NS1|
|LRR||Leucine Rich Repeat|
|Opsin||Opsin Seed Alignment|
|RuBisCo_Large||Ribulose bisphosphate carboxylase large chain, catalytic domain|
|RuBisCo_Large_N||Ribulose bisphosphate carboxylase large chain, N-terminal domain|
|RVT_Thumb||Reverse transcriptase thumb domain|
|ZF-C2H2||Zinc finger, C2H2 type|