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Reply from Sudhir:
Dear Barry:
It is nice to hear from you. Here are the answers to your specific questions.
(1) Do you plan to add either maximum likelihood or Bayesian methods of phylogenetic tree reconstruction in the near future?
Answer: With MEGA3.5 release scheduled very soon, users will have a Maximum Composite Likelihood (MCL) method for estimating evolutionary distances, building phylogenetic trees (using distances), and inferring the pattern of nucleotide substitutions. In MEGA4.0, we will release a version that will integrate PAML for specific calculations: including test of molecular clock, finding the most suitable model for nucleotide sequence evolution, and other likelihood ratio tests. Therefore the PAML inclusions are aimed at testing evolutionary patterns, rather than searching for phylogenies using the usual ML approaches. In the next version, our plan is to provide an intuitive interface into \"multidivtime\" to estimate time of species divergence. I can provide more details if you need it for specific purposes (as this release schedule is not public knowledge).
(2) What resources would be required in order to port Mega3 to Macintosh OSX and to Linux?
Answer: MEGA has an extensive user-interface, which is the hardest part to port to OS X and Linux. Therefore, we are currently planning a web-server version of MEGA to get around this. However, its release schedule is not yet firmly decided.
(3) When do you anticipate releasing the PDF version of the manual?
Answer: I expect to release a PDF version of the manual by MEGA4.
with best regards
Sudhir |
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