This tool automatizes the deconvolution of the mixed traces obtained when Sanger-sequencing mixtures of PCR products of different lengths (for details, see Flot J-F, Tillier A, Samadi S, Tillier S (2006) Phase determination from direct sequencing of length-variable DNA regions. Molecular Ecology Notes 6:627–630 and Flot J-F (2007) Champuru 1.0: a computer software for unraveling mixtures of two DNA sequences of unequal lengths. Molecular Ecology Notes 7:974–977 for details).
This tool allows users to generate easily PHASE input files from FASTA sequences alignemnts and convert PHASE output files back into FASTA (as detailed in Flot J-F (2010) SeqPHASE: a web tool for interconverting PHASE input/output files and FASTA sequence alignments. Molecular Ecology Resources 10:162–166).
This web tool allows users to generate quickly publication-quality haplowebs (short for "haplotype webs"), see Flot J-F, Couloux A, Tillier S (2010) Haplowebs as a graphical tool for delimiting species: a revival of Doyle’s “field for recombination” approach and its application to the coral genus Pocillopora in Clipperton. BMC Evolutionary Biology 10:372 and Spöri Y, Flot J (2020) HaplowebMaker and CoMa: two web tools to delimit species using haplowebs and conspecificity matrices. Methods in Ecology and Evolution for details). A detailed FAQ is also available.
This web tool automatizes the production of conspecicity matrices from partition matrices (produced e.g. using HaplowebMaker. For details, see Spöri Y, Flot J (2020) HaplowebMaker and CoMa: two web tools to delimit species using haplowebs and conspecificity matrices. Methods in Ecology and Evolution and the FAQ
Bcool implements a graph-based approach to short-read correction that is more accurate than classical k-mer spectrum-based approaches. For details, see Limasset A, Flot J-F, Peterlongo P (2020) Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs. Bioinformatics 36:1374–1381