- final static private String HELP_OPTION_1 = "help";
- final static private String HELP_OPTION_2 = "h";
- final static private String REMOVE_WORST_OFFENDERS_OPTION = "w";
- final static private String AV_GAPINESS_OPTION = "a";
- final static private String STEP_OPTION = "s";
- final static private String LENGTH_OPTION = "l";
- final static private String REALIGN_OPTION = "r";
- final static private String PRG_NAME = "msa_compactor";
- final static private String PRG_DESC = "multiple sequnce aligment compactor";
- final static private String PRG_VERSION = "0.01";
- final static private String PRG_DATE = "140221";
- final static private String E_MAIL = "phylosoft@gmail.com";
- final static private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester";
+ final static private String HELP_OPTION_1 = "help";
+ final static private String HELP_OPTION_2 = "h";
+ final static private String REMOVE_WORST_OFFENDERS_OPTION = "r";
+ final static private String AV_GAPINESS_OPTION = "g";
+ final static private String STEP_OPTION = "s";
+ final static private String LENGTH_OPTION = "l";
+ final static private String REALIGN_OPTION = "a";
+ final static private String PATH_TO_MAFFT_OPTION = "mafft";
+ final static private String DO_NOT_NORMALIZE_FOR_EFF_LENGTH_OPTION = "nn";
+ final static private String PRG_NAME = "msa_compactor";
+ final static private String PRG_DESC = "multiple sequnce aligment compactor";
+ final static private String PRG_VERSION = "0.01";
+ final static private String PRG_DATE = "140314";
+ final static private String E_MAIL = "phylosoft@gmail.com";
+ final static private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester";