# HG changeset patch # User greg # Date 1493657464 14400 # Node ID 9b78e5c2a14e9e3c1ba5094358481bc93c35eaec # Parent 715ca3160a2767da9baacab56f3b89bc0459c86a Uploaded diff -r 715ca3160a27 -r 9b78e5c2a14e kaks_analysis.xml --- a/kaks_analysis.xml Mon May 01 12:41:36 2017 -0400 +++ b/kaks_analysis.xml Mon May 01 12:51:04 2017 -0400 @@ -219,7 +219,7 @@ - **match score** - number of base matches in a pairwise sequence alignment divided by the length of shorter sequence. Positions in the alignment corresponding to gaps are not considered. The score is restricted to the range 0.3 - 1.0. - - **Species rates recalibration configuration** - select 'Yes' to recalibrate synonymous substitution rates of a species using a predetermined evolutionary rate. Recalibration evolutionary rate can be determined from a species tree inferred from a collection of conserved single copy genes from taxa of interest as described in Cui et al., 2006. Rate recalibration applies only to paralogous comparisons. + - **Species rates recalibration configuration** - select 'Yes' to recalibrate synonymous substitution rates of a species using a predetermined evolutionary rate. Recalibration evolutionary rate can be determined from a species tree inferred from a collection of conserved single copy genes from taxa of interest as described in [7]. Rate recalibration applies only to paralogous comparisons. - **recalibration rate** - a predetermined evolutionary recalibration rate. @@ -291,5 +291,15 @@ number = {2}, pages = {1-14},} + + @article{Cui2006, + journal = {Genome Research}, + author = {7. Cui L, Wall PK, Leebens-Mack JH, Lindsay BG, Soltis DE, Doyle JJ, Soltis PS, Carlson JE, Arumuganathan K, Barakat A, Albert VA}, + title = {Widespread genome duplications throughout the history of flowering plants}, + year = {2006}, + volume = {16}, + number = {6}, + pages = {738-749},} +