Sentence examples for using the phylip package from inspiring English sources

Dendograms were drawn using the PHYLIP package [23].

All phylogenetic analysis was carried out using the PHYLIP package, as implemented in the MOBYLE Portal (http://mobyle.pasteur.fr/) [23].

We first aligned the sequences using ClustalX [33] and generated a maximum likelihood tree using the PHYLIP package [34].

The neighbour joining tree was produced using the PHYLIP package [48] and based on the consensus of 1000 bootstrap replicates.

Using the PHYLIP package [30], a hierarchical tree-like representation of these data can be generated using the Fitch-Margoliash distance-based optimization method.

A phylogenetic tree constructed using the PHYLIP package suggests that these 14 Puf proteins can be grouped into three clusters: (1) the Puf-A homolog cluster, (2) the C14orf21 homolog cluster, and (3) the PUM1/PUM2 homolog cluster (Fig. 2B).

The second approach used the phylip package [ 28] to apply a distance-based bootstrap analysis with 1000 replicates to each of the curated alignments.

We used the Phylip package V3.69 [ 66] to build the maximum likelihood (ML) tree for each protein family under the JTT substitution model.

Bootstrap values were obtained for branching patterns using the Phylip software package (version 3.65 [103]) and values ≥50% were included for main nodes of the tree.

Additional phylogenetic analyses were performed using the PHYLIP software package (version 3.5c; Felsenstein 1993).

The neighbor-joining (NJ) method was performed with JTT amino acid substitution matrix using the Phylip software package [ 79].