MACSE Options

Allowed nucleotides Unidentified nucleotides URL : samples/delegations/nucleos/allow_NT/ Nucleotides alignments may contain inexistent nucleotides which can prevent MACSE from working correctly, you can bypass this problem using the allow_NT option : This example will read allow_NT nucleotides as if they were ‘N’ letters. Note that some characters can be misinterpreted by the console, so it is … Lire la suite

Compressed amino acid alphabet Folder: samples/delegations/alphabet/ In some MACSE subprograms, you can use the alphabet_AA option to change the default compressed amino acid alphabet used by MACSE to compute initial pairwise distances or to identify homologous fragments. For instance the command to select the Dayhoff_6 alphabet is: The proposed alphabets are those listed in the … Lire la suite

Alignment cost parameters MACSE defines the score/cost of a nucleotide alignment based on its amino acid translation. The cost of an alignment depends on the elementary costs of the events it encompassed: MACSE provides some default values, but you can set all those costs at another value. Note that: 1. names of the cost options … Lire la suite

Genetic codes and translation 1. Selecting the adapted genetic code(s) Folder: samples/delegations/aminos/gc_def/ MACSE is able to handle the following genetic codes: By default MACSE uses The_Standard_Code but you can specify a different default genetic code for your dataset using the gc_def option, specifying the number of the genetic code (listed above): For instance, to align … Lire la suite