Most people go for BLAST and FASTA.

It all depends on your goals. I'd start with a linux box. Here are some basic tools installed on mine:

BIOPIECES : OK

subversion client - "svn: OK

PERL : OK

PERL:Inline : OK

PERL:JSON::XS : OK

PERL:SVG : OK

PERL:Bit::Vector : OK

PERL:Time::HiRes : OK

Ruby : OK

RubyGem:gnuplot : OK

RubyGem:narray : OK

RubyGem:RubyInline : OK

RubyGem:Bio-blastxmlparser: ?

blastall : OK

blat : OK

bwa : OK

bowtie : OK

formatdb : OK

gnuplot : OK

idba : WARNING

muscle : OK

mummer : OK

mysql : OK

prodigal : OK

Ray : OK

scan_for_matches : WARNING

usearch : WARNING

velveth : OK

velvetg : OK

vmatch : WARNING

PAGIT : OK

Artemis : OK (nnotation & BAM visualization tool - version Dec2011)

ACT : OK (DNA sequence comparison viewer v. Dec2011)

BLASTALL : OK (Blast version 2.2.15)

MUMmer : OK (sequence comparison tools - version 3.22)

SAMTOOLS : OK (short read mapper BAM/SAM files) version 1.0.19

SMALT : OK (read mapping tool (k-mer based) - version 0.5.3)

VELVET : OK (short read assembler - version 1.1.06)

FastQC : OK (qality assess fastq file)

fastx-toolkit 0.0.12 : OK

Homer Tools : OK

Bioperl : OK

Biopython : OK

Ray 2.2.0 : OK (assembler)

usearch : OK

Bowtie2 2-2.1.0 : OK (read mapper)

CAP3 : OK (long read assembler)

Jellyfish : OK (k-mer counting)

ea-utils.1.1.2-537 : OK (adapterscan, demultiplex, and joining fastq files)

SSPACE : OK (extend contigs of assembly using paired end reads)

Cython : OK

Pysam : installed (untested)

SciPy : OK

NumPy : OK

EMIRGE : installed (untested)

ncbi-blast-2.2.28+ : OK

HMMER 3.0 : installed (untested)

MEGAN 4 : OK

multi-metagenome : deployed (untested; not in path)

Rstdudio : OK

R : OK

R(knitr) : OK

R(vegan) : OK

R(plyr) : OK

R(RColorBrewer) : OK

R(alphahull) : OK

R(ggplot2) : OK

Hi daniel,

You can use QIIME pipeline for your genome analysis.

Hi

You can use ACT from Sanger to compare genomes. Didactic and easy!!!

For comparison of WGS data, you can use tools like Mauve, MUMMER, BLAST, ACT (Artemis Comparison Tool), etc.

I am not sure what your goal is.

You wish to compare whole genome sequences to predict structures and design primers for the genes?

I mean, what genes are you targeting specifically?

What do you mean by gene structures?