MEGA has problems reading the NEXUS/PAUP format file smoothly
MEGA3 stops responding or crashes while performing Maximum Parsimony analyses with bootstrap.
When performing the MP method, more than one tree with different topologies can be obtained. All trees display the same topology when exported in Newick format, although this is not the case when viewed in Tree Explorer.
Division by zero error appears in calculation of TajimaD.
MEGA3 crashes when performing ClustalW in larger multiple alignments.
The "selection tests" menu doesn't update when genes/domains are marked coding or uncoding.
Broken bug report link on MEGA 3 FAQ page.
The release build still contains expiration date.
Error reading Newick tree files containing bootstrap values.
Some bootstrap consensus trees remain stuck
in "topology only" mode
when recovered from *.mts tree session files.
Rate not updated after changing the calibration point and
pressing the OK button in Calibrate-Clock.
ClustalW access violation when aligning large data sets.
Standard genetic code table
always loaded by Alignment Explorer regardless of user's code table selection.
Fail to do Blast search from MEGA due to NCBI's changes to Blast interface (Fixed in MEGA#4022).
Failed to export non-interleaved format sequence data.
File converter appends data to existing files instead of overwriting
The cutoff value for generating a bootstrap consensus NJ (ME, MP) tree does not work.
Division by zero error occurs when changing tree explorer options.
Tree explorer loses user-specified ordering during compress/decompress.
Compression state of tree nodes not recovered from tree session.
Incorrect drawing of radiation trees recovered from some *.mts tree session files.
Unable to display bootstrap consensus tree in radiation format.
Tree Explorer initializes in minimized state.
Fail to display radial tree after branch collapse. (Fixed in MEGA#4022)