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how to create "sample file" for the qAlign() function after trimming the reads in R

The QuasR vignette tells you how to run it. The samples file should contain a list of your samples and fastq files.
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1 vote

Phylogenetic tree building from proGenomes database for shotgun metagenomics

I would not recommend the approach that you describe. I am not sure that I completely understand it. For example, metagenomic binning by e.g. MetaBAT is not a scaffolding operation, which returns a ...
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Why must a maximal non-branching path be a contig?

The definition of contig is derived from assembly algorithms. A contig is not necessarily present in the genome. PS: i.e. "contig" is algorithmically defined, not biologically defined. Is ...
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What is the different between the I-TASSER, phyre2, SWISS-model in the 3D tertiary structure?

This is a common Q. Briefly, you have some techniques here that get used separately or combined: Ab initio: assemble the protein from scratch, often via a library fragmented peptides (3-mer, 6-mers, ...
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