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Fig. 4 | BMC Bioinformatics

Fig. 4

From: LMAP: Lightweight Multigene Analyses in PAML

Fig. 4

Interactive functioning of omap.pl - User Table. The resulting CSV table containing the BM data from imap.pl, where each row contains the absolute path to the corresponding codeml results file in the directory structure. This path is decomposed in columns by omap.pl, whereby each subfolder name constitutes a column. This additional on-screen information complements the codeml maximum likelihood parameter estimates simplifying overall data perception, advantageous for organization processes. At the top, for simpler use across the interactive commands, the column names (in red) are shown as “C + number” (see also Fig. 5), whereas the original CSV column names, are revealed, through the command “fh” (Additional file 2: Figure S7). It is possible to adjust visible table information, by scrolling and by (un)hiding columns or defining number of visible rows. Below the table, from left to right, various information is shown (in cyan), such as the total number of rows and of columns, the number of selected rows, the number of visible rows and the number of hidden columns. Scrolling information is shown below; activate scroll by typing “Ctrl-d”, use arrow keys to scroll up or down, “Home” key to go to top or “End” key to go to bottom. When finished, deactivate scroll by typing “Ctrl-\”, to enable interactive commands processing. Below, the table currently shown (“User Table”) is indicated by the letter “U” (in red) in the OMAP PROMPT line. The interactive commands are consulted in two ways, either through a help screen, triggered by entering the “?” command, or through the CLO “--help” (as in omap.pl --help), which will print the help into a text file in the current directory (see Additional file 2: Figures S6 and S7)

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