satDNA Analyzer

User Manual

The input file for satDNA Analyzer can be made of many aligned sequences from two different species. The user can remove any sequence for the analysis just by adding the character (%) at the beginning of the species name alignment in the input file. Sites containing alignment gaps can be either included or excluded. Missing data are considered as ignored positions and they are completely excluded for the analysis.

The name of species should have an ID tag at the beginning of the name. Automatically, user will be asked to enter an ID for each species. A valid ID should include a specific feature of each species name. Sequences belonging to the same species do not need to be sequentially ordered in the alignment.

The program generates two outputs.

• The first output file is presented in html format including two parts. The first part consists of a multicoloured alignment identifying the different nucleotide sites according to their classification as monomorphic or polymorphic, discriminates shared from non-shared polymorphisms and classifies each non-shared polymorphism within each of the Strachan's stages of transition. This part also includes a summary of the sites belonging to each category and their location along the sequence, as well as three consensus sequences (corresponding to both species and a global one) and AT richness estimation. The second part of the output file includes the computation of some measures of the extent of DNA divergence between the two species compared as well as measures of the intra-specific polymorphism and variability.
• The second output file is the sequence alingment without shared polymorphisms in the same format than input file.

Notes to Syntax

• input_file: file where the sequences for the species are stored. satDNA Analyzer recongnizes sequences belonging to two different species according to a specific ID. User will be required to enter one ID for each species. Please, note that ID should be a name common to all sequences belonging to one species and not present in the other one. Furthermore, ID should be at the beginning of the name, if not, satDNA Analyzer will recognize the two groups of species and give a correct output, but changes in sequence names may be expected in some output fomats.
• output_file: file where the results will be stored. It has to be an html file (.html) for the correct visualization of the results and should be placed in the same folder than satDNA.css file for graphic representation view. If the file does not exist it will be automatically created, if it already exists it will be overwritten. Automatically, the program will generate a second .txt output containing the alignment without shared polymorphisms in the same format than input file.
• T/lambda: this is an optional argument. It takes either the time divergence between the two species, T, or lambda, rate of nucleotide substitutions per time per year and calculates the corresponding value.
• exclude_polymorphic_positions: values (0|1). This argument must be set to 1 if the user wants to exclude polymorphic positions for further analysis. It must be set to 0 otherwise.
• complete_deletion_pairwise: values (0|1). It must be set to 0 if the user wants to use the pairwise option. It must be set to 1 for the complete deletion option.