PyElph

[…] analysis []. next, this similarity matrix was used to construct the phylogenetic tree through upgma (unweighted pair group method with arithmetic mean) method with a distance tool using the free pyelph 1.4 computer software [,,]. the robustness of the dendrogram was further checked by the cophenetic correlation coefficient. the cophenetic correlation coefficient was calculated using […]

[…] sequential steps: dna was extracted, checked for purity, integrity and ribotyped by published protocols [–].subsequently, the polyacrylamide gel electrophoresis (page) images were analysed by pyelph software []. bands across the lanes were matched based on position and number of bands, and a binary matrix, designating presence of band as ‘1’ and absence as ‘0’, was made using […]

[…] and eric-reverse (5′aagtaaggactggggtgagcg-3′), was performed as described earlier (versalovic et al., ). bio-red gel doc system was used to scan gel image and analyzed the bands by pyelph version 1.4 software to generate a dendrogram by the un weighted pair group method using arithmetic averages (upgma) clustering (pyelph) (pavel and vasile, )., of 44 isolates, escherichia coli […]

[…] positions of the bands on the different lanes and gels. the existence of a given band was coded as 1 and the lack of a given band was coded as 0 in an information matrix and analyzed using the pyelph 1.4 software (bmc bioinformatics u.s). dendrograms of differences were set up for each case., mdr was explained as obtained insusceptibility to at least one agent in three […]

[…] it gave the best banding pattern. rapd typing was then performed using selected isolates (additional file ). the resulting gel was photographed under uv light. rapd fingerprints were analysed with pyelph version 1.4 gel analysis software [], and a dendrogram generated using the unweighted pair group method with arithmetic averages (upgma)., following initial testing, 52 k. pneumoniae isolates […]