NEWS

---

scoup 1.1.1

• Improved flexibility by allowing specification of mutation rate parameters.
• Adjusted the 'fixed' input in 'codonCoeffs' function.
• Reversed the mutation matrix flexibility due to expensive computational cost.
• Updated help files to aptly emphasise episodic in-place of "deterministic".
• Revised the 'codonFreq' function so that it uses 'softmax' identity.

scoup 0.99.16

• Edited citation and vignette appropriately

scoup 0.99.15

• Incorporated recommendations from @jianhong
• Updated 'biTree' to include test and warning

scoup 0.99.2

• Updated temporary inst/CITATION file.
• Updated seqDetails.R to accommodate NOTE from Bioc report about use of "is".
• Updated NAMESPACE as recommended by Bioc report: imported "methods" & "is".
• Incorporated Biostrings: used to generate colorful sequences.
• Initiated unit tests.

scoup 0.99.1

• Updated temporary inst/CITATION file.
• Deleted redundant LICENSE file.
• Removed patchlevel dependency attached to R in DESCRIPTION file.
• Shortened code lengths and corrected T/F.
• Adjusted spaces to size 4.
• Bumped package version number to *.**.1.

scoup 0.99.0

• Submitted on Bioconductor for review.
• Edited the DESCRIPTION, README and vignettes with Bioconductor-esque installation instructions.