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.



Protein Name Description
ABC_Tran ABC transporter
Ank Ankyrin repeat
Cox1 Cytochrome C and Quinol oxidase polypeptide I
Cytochrom_B_C Cytochrome b(C-terminal)/b6/petD
Cytochrom_B_N Cytochrome b(N-terminal)/b6/petB
Globin Globin Seed Alignment
GP120 Envelope glycoprotein GP120
GP120 Yamaguchi alignment GP120
HVC_NS1 Hepatitis C virus non-structural protein E2/NS1
Immunoglobulin Immunoglobulin domain
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 Reverse transcriptase
RVT_Thumb Reverse transcriptase thumb domain
ZF-C2H2 Zinc finger, C2H2 type