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Positive selection & conservation in protein-coding sequences

Goals:

Detect if my sequences were affected by positive or negative selection (average, site-specific or lineage-specific)

Why:

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.

Input data:

Aligned or non-aligned protein-coding sequences (DNA-data starting with first codon position, sequence length should be a multiple of 3).

Pipeline:

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

Deliverables:

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).
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