Positive selection & conservation in protein-coding sequences
Detect if my sequences were affected by positive or negative selection (average, site-specific or lineage-specific)
Selective pressures shape genomic sequences, revealing signals of adaptation to new pathogens or new environments, co-evolution and diversification in host-pathogen's arms race may be achieved.
Aligned or non-aligned protein-coding sequences (DNA-data starting with first codon position, sequence length should be a multiple of 3).
1. Align protein-coding sequences
2. Infer phylogeny
3. Conduct likelihood ratio tests for positive selection
4. Summarize Bayesian prediction of site categories
5. Interpret the results
Description of positive and negative selection pressures for a multiple sequence alignment, including classification of positive/negative selected sites or lineages (dependent on type of analyses/ hypotheses that were tested).