I am looking for a straight-forward way to compare metabolic pathways (presence and absence enzymes) in several annotated but not yet published bacterial genomes, it should be non-commercial and can be command-line based.
The ideal output would be a map for each pathway (Kegg-like), colored depending on presence or absence in the input genomes, with data from multiple genomes in one map (and colors changing if an enzyme is present in all of the input genomes).
It depends on how to you want to present your data. If you just want to show the summary statistics on the presence of enzymes (or genes/proteins) in multiple genomes, you may use pathview directly. In other words, if you want to color the presence of enzymes in N genomes into N+1 (0,1,2.. N) different levels, you may check the discrete data examples like Figure 6 in the package vignette or tutorial, http://bioconductor.org/packages/release/bioc/html/pathview.html.
Similarly, pathview can visualize metagenomic or microbiome data when the data are mapped to KEGG ortholog pathways (gene IDs in the format of Kxxxxx). In fact, pathview can visualize various types of molecular data, either continuous or discrete, as long as the data can be mapped onto pathways.
If you want to show the presence absence of enzymes of N genomes side by side by dividing each enzyme nodes into N pieces, pathview does not provide the function currently.
interactive Pathways Explorer (iPath) is a web-based tool for the visualization, analysis and customization of the various pathways maps. Current version provides three different global overview maps:
Metabolic pathways: constructed using 146 KEGG pathways, and gives an overview of the complete metabolism in biological systems
Regulatory pathways: 22 KEGG regulatory pathways
Biosynthesis of secondary metabolites: contains 58 KEGG pathways involved in biosynthesis of secondary metabolites
In addition to the KEGG based overview maps, iPath is used for visualization of various species specific, manually created pathway maps. At the moment, only Mycoplasma pneumoniae and a beta version of Mycobacterium tuberculosis maps are publicly available.
iPath provides extensive map customization and data mapping capablities. Colors, width and opacity of any map element can be customized using various types of data (for example KEGG KOs, COGs or enzyme EC numbers). Our help pages provide the full list of supported data types and required formats. All maps in iPath can be easily converted to various bitmap and vector graphical formats for easy inclusion is your documents or further processing.
This software has been used in comparison of bacterial communities from different soil depths, for example.
EDIT: Sorry, I realise that you said it should be command-line based and this is only available via a web interface but if you contact them, you may be able to get a command-line version..?