What is a simple command line tool for doing Needleman-Wunsch pair-wise alignment on the command line I have two DNA strings:  


  GGAGGAGGGAGAAGGAGGGAGGGAAGAGGAGGGAGAAGGAGGGAGGC 


and


  AGAAGGAGGGAGGGAAGAGGAGGGAGAAGGAGGGAGGGAAGAGGAGG


I want a tool that allows me to do something like this on the command line:

$ aligner  GGAGGAGGGAGAAGGAGGGAGGGAAGAGGAGGGAGAAGGAGGGAGGC AGAAGGAGGGAGGGAAGAGGAGGGAGAAGGAGGGAGGGAAGAGGAGG


and receive an ASCII visualization of a pairwise alignment. Something like this would work:

GGAGGAGGGAGAAGGAGGGAGGGAAGAGGAGGGAGAAGGAGGGAGGC---------
---------AGAAGGAGGGAGGGAAGAGGAGGGAGAAGGAGGGAGGGAAGAGGAGG


I prefer a tool that is packaged on bioconda. A tool that also does protein and RNA sequences is even more preferable.
You are looking for the needle program from the EMBOSS suite. Available in bioconda. 

http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/needle.html

To read sequences from the commandline, you need so specify the format as asis. To get the output on the screen, you'll need -stdout and to use the default alignment parameters (gap penalty 10, extend_penalty 0.5) you'll need -auto. Thus your query above would be:

$ needle -asequence asis:GGAGGAGGGAGAAGGAGGGAGGGAAGAGGAGGGAGAAGGAGGGAGGC -bsequence asis:AGAAGGAGGGAGGGAAGAGGAGGGAGAAGGAGGGAGGGAAGAGGAGG -auto -stdout
########################################
# Program: needle
# Rundate: Tue 27 Nov 2018 10:48:50
# Commandline: needle
#    -asequence asis:GGAGGAGGGAGAAGGAGGGAGGGAAGAGGAGGGAGAAGGAGGGAGGC
#    -bsequence asis:AGAAGGAGGGAGGGAAGAGGAGGGAGAAGGAGGGAGGGAAGAGGAGG
#    -auto
#    -stdout
# Align_format: srspair
# Report_file: stdout
########################################

#=======================================
#
# Aligned_sequences: 2
# 1: asis
# 2: asis
# Matrix: EDNAFULL
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 56
# Identity:      37/56 (66.1%)
# Similarity:    37/56 (66.1%)
# Gaps:          18/56 (32.1%)
# Score: 181.0
# 
#
#=======================================

asis               1 GGAGGAGGGAGAAGGAGGGAGGGAAGAGGAGGGAGAAGGAGGGAGGC---     47
                              |||||||||||||||||||||||||||||||||||||.   
asis               1 ---------AGAAGGAGGGAGGGAAGAGGAGGGAGAAGGAGGGAGGGAAG     41

asis              47 ------     47

asis              42 AGGAGG     47


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