I can't help with the cfasta conversion, but I can with the annotation portion. There are basically two types of annotation that you might be referring to de novo or variant annotation. I'll try and describe both.
If this is a newly sequenced organism and you are doing de novo annotation (i.e no existing reference genome), you can use MAKER for structural annotation as well as MAKER and InterProScan for functional annotation. Also look at gmod.org for other annotation tools from the generic model organism database project.
If this is a human genome (or an organism with an existing reference genome), and you want to annotate functional variants, use BWA to align to the reference, GATK or samtools to identify and variants (SNPs and indels). Then use VAAST or annonovar to classify and prioritize the variants.