A,B   C    D      E,F,G     H,I,L     M     N,O     P     R     S T,V,W,Y

P1 Clones – Hypercard stack for keeping track of clones that were constructed with the bacteriophage P1 cloning system (M)

PAML – Phylogenetic Analysis by Maximum Likelihood (PAML) (M, W, U)

PcFold – Predicts stem and loop regions of RNA structures (W)

PHYLIP – A PHYLogeny Inference Package for phylogenetic analysis (M, W, U)

Phylodendron – Application for drawing phylogenetic trees (M, W, U) (java)

Phyltest – Testing phylogenetic hypothesis, with the comparison of three alternative phylogenetic trees, estimation of average pairwise distances and others (W)

Plasmid Processor – Tool for plasmid presentation for scientific and educational purposes (W)

Plasmid-Maker – Draws linear and circular plasmid maps, allows borders of various widths and fills of grays, arrows and other options (M)

PrimerDesign – DOS program to choose primer for PCR or oligonucleotide probes (W)

Primer – Program for automatically selecting PCR primers (M, W, U)

Primer-Master – Automatically search and selection of optimal primers and primers pair for various variants of PCR (W)

Primers! – Allows users to interactively scroll through lists of forward and reverse primers to pick exactly the primer pair wanted (M)

ProAnal – Analysis of multiple protein alignments, studying the structure-function and structure-activity relationships in protein/peptide families (W)

ProAnalyst – Investigation of structural differences between proteins divided by functional, evolutionary, or other criteria (W)

ProAnWin – Multiple sequence alignment, analysis of protein sequences and structures, structure-activity relationships, design of protein-engineering experiments (W)

ProfileGraph – A graphical protein analysis tool (W)

PromFind – Accepts a DNA sequence and adds a feature table to annotate the location of putative promoter regions (W)

ProMSED – Automatic and manual DNA and protein sequence alignment, editing, comparison and analysis (W)

Prophet – Advanced, easy-to-use software for data management and visualization and statistical analysis (W, U)

Protein Sequence Analysis - Sequence editor (W)

Puzzle – Maximum likelihood analysis for nucleotide, amino acid and two-state data (M, W, U)