Sequences don’t have their complete name while opening in CodonCode Aligner
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There may be a space in the name
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Remove all of the spaces in the name and reopen the data set
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All sequences failed to assemble in a single contig
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There may not be enough identity between the reference and query sequences
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Assign another reference sequence from the unassembled sequences
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The Perl script failed to convert Fasta to Phylip format
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There may be illegal symbols in the sequence characters or names
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Remove any illegal symbol from the sequence by opening the data set in TextEdit, and save before closing
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RAxMLGUI installation is incomplete
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The library is missing
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To speed up the algorithm you may need to install a library from the program webpage
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Load of alignment in RAxMLGUI failed
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There may be illegal symbols in the sequence characters or names
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Remove any illegal symbol from the sequence by opening the data set in TextEdit, and save before closing
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| Problem specific to each program |
There may be unseen problems associated with each program |
Consult the respective webpage for appropriate tutorial and help |
